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  "site": {
    "name": "Bactopia",
    "url": "https://bactopia.github.io",
    "tagline": "An extensive workflow to process Nanopore and Illumina sequencing for bacterial genomes."
  },
  "generated": "2026-04-25T04:33:48Z",
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          "description": "Bactopia Tool: Amrfinderplus.",
          "url": "https://bactopia.github.io/bactopia-tools/amrfinderplus",
          "path": "/bactopia-tools/amrfinderplus",
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            "bactopia-tool"
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          "description": "Gene identification through local assemblies.",
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          "path": "/bactopia-tools/ariba",
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        {
          "title": "bakta",
          "description": "Rapid annotation of bacterial genomes and plasmids.",
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          "path": "/bactopia-tools/bakta",
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          "url": "https://bactopia.github.io/bactopia-tools/blastn",
          "path": "/bactopia-tools/blastn",
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            "bactopia-tool"
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            "bactopia-tool"
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        {
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          "description": "Search against protein BLAST databases using translated nucleotide queries.",
          "url": "https://bactopia.github.io/bactopia-tools/blastx",
          "path": "/bactopia-tools/blastx",
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            "translation",
            "bactopia-tool"
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            "bactopia-tool"
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          "path": "/bactopia-tools/btyper3",
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            "bactopia-tool"
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          "title": "defensefinder",
          "description": "Systematic identification of anti-phage defense systems.",
          "url": "https://bactopia.github.io/bactopia-tools/defensefinder",
          "path": "/bactopia-tools/defensefinder",
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            "hmm",
            "protein-domains",
            "bactopia-tool"
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          "description": "Functional annotation of proteins using orthologous groups and phylogenies.",
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          "url": "https://bactopia.github.io/bactopia-tools/emmtyper",
          "path": "/bactopia-tools/emmtyper",
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          "path": "/bactopia-tools/fastani",
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          "path": "/bactopia-tools/gamma",
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          "path": "/bactopia-tools/hpsuissero",
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          "url": "https://bactopia.github.io/bactopia-tools/ismapper",
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            "bactopia-tool"
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          "description": "Comprehensive screening of Klebsiella genomes for virulence and resistance determinants.",
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          "path": "/bactopia-tools/kleborate",
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          "description": "Sequence Based Typing (SBT) of Legionella pneumophila.",
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          "title": "mashdist",
          "description": "Calculate Mash distances between sequences and reference genomes.",
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          "description": "Rapid phylogenetic tree construction using Mash distances.",
          "url": "https://bactopia.github.io/bactopia-tools/mashtree",
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          "title": "meningotype",
          "description": "Comprehensive typing of Neisseria meningitidis.",
          "url": "https://bactopia.github.io/bactopia-tools/meningotype",
          "path": "/bactopia-tools/meningotype",
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          "title": "merlin",
          "description": "MinMER-assisted species-specific tool selection and execution.",
          "url": "https://bactopia.github.io/bactopia-tools/merlin",
          "path": "/bactopia-tools/merlin",
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          "title": "midas",
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          "url": "https://bactopia.github.io/bactopia-tools/midas",
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            "midas",
            "bactopia-tool"
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          "source_file": "bactopia-tools/midas.mdx"
        },
        {
          "title": "mlst",
          "description": "Automatic Multi-Locus Sequence Type (MLST) calling from assembled contigs.",
          "url": "https://bactopia.github.io/bactopia-tools/mlst",
          "path": "/bactopia-tools/mlst",
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            "alleles",
            "pubmlst",
            "bactopia-tool"
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          "source_file": "bactopia-tools/mlst.mdx"
        },
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          "title": "mobsuite",
          "description": "Reconstruction and annotation of plasmids from bacterial genome assemblies.",
          "url": "https://bactopia.github.io/bactopia-tools/mobsuite",
          "path": "/bactopia-tools/mobsuite",
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            "bactopia-tool"
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          "source_file": "bactopia-tools/mobsuite.mdx"
        },
        {
          "title": "mykrobe",
          "description": "Antimicrobial resistance detection for specific bacterial species.",
          "url": "https://bactopia.github.io/bactopia-tools/mykrobe",
          "path": "/bactopia-tools/mykrobe",
          "tags": [
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        },
        {
          "title": "ngmaster",
          "description": "Multi-antigen sequence typing of Neisseria gonorrhoeae.",
          "url": "https://bactopia.github.io/bactopia-tools/ngmaster",
          "path": "/bactopia-tools/ngmaster",
          "tags": [
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            "ng-mast",
            "typing",
            "bactopia-tool"
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          "source_file": "bactopia-tools/ngmaster.mdx"
        },
        {
          "title": "pangenome",
          "description": "Pangenome analysis with optional core-genome phylogeny.",
          "url": "https://bactopia.github.io/bactopia-tools/pangenome",
          "path": "/bactopia-tools/pangenome",
          "tags": [
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            "pan-genome",
            "phylogeny",
            "comparative-genomics",
            "bactopia-tool"
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          "source_file": "bactopia-tools/pangenome.mdx"
        },
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          "title": "pasty",
          "description": "In silico serogrouping of Pseudomonas aeruginosa isolates.",
          "url": "https://bactopia.github.io/bactopia-tools/pasty",
          "path": "/bactopia-tools/pasty",
          "tags": [
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        {
          "title": "pbptyper",
          "description": "Penicillin Binding Protein (PBP) typing for Streptococcus pneumoniae.",
          "url": "https://bactopia.github.io/bactopia-tools/pbptyper",
          "path": "/bactopia-tools/pbptyper",
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        {
          "title": "phispy",
          "description": "Prediction of prophages in bacterial and archaeal genomes.",
          "url": "https://bactopia.github.io/bactopia-tools/phispy",
          "path": "/bactopia-tools/phispy",
          "tags": [
            "prophage",
            "phage",
            "annotation",
            "bacterial",
            "archaeal",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/phispy.mdx"
        },
        {
          "title": "plasmidfinder",
          "description": "Bactopia Tool: Plasmidfinder.",
          "url": "https://bactopia.github.io/bactopia-tools/plasmidfinder",
          "path": "/bactopia-tools/plasmidfinder",
          "tags": [
            "plasmid",
            "identification",
            "replicon",
            "typing",
            "assembly",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/plasmidfinder.mdx"
        },
        {
          "title": "pneumocat",
          "description": "Capsular type assignment to Streptococcus pneumoniae from sequence reads.",
          "url": "https://bactopia.github.io/bactopia-tools/pneumocat",
          "path": "/bactopia-tools/pneumocat",
          "tags": [
            "streptococcus-pneumoniae",
            "capsular-typing",
            "pneumocat",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/pneumocat.mdx"
        },
        {
          "title": "prokka",
          "description": "Rapid whole genome annotation of bacterial, archaeal, and viral genomes.",
          "url": "https://bactopia.github.io/bactopia-tools/prokka",
          "path": "/bactopia-tools/prokka",
          "tags": [
            "annotation",
            "genome",
            "prokaryote",
            "functional-annotation",
            "genes",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/prokka.mdx"
        },
        {
          "title": "quast",
          "description": "Quality assessment of assembled contigs using QUAST.",
          "url": "https://bactopia.github.io/bactopia-tools/quast",
          "path": "/bactopia-tools/quast",
          "tags": [
            "assembly",
            "quality",
            "assessment",
            "metrics",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/quast.mdx"
        },
        {
          "title": "rgi",
          "description": "Prediction of antibiotic resistance genes using RGI.",
          "url": "https://bactopia.github.io/bactopia-tools/rgi",
          "path": "/bactopia-tools/rgi",
          "tags": [
            "bacteria",
            "antibiotic-resistance",
            "card",
            "resistance-genes",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/rgi.mdx"
        },
        {
          "title": "sccmec",
          "description": "Typing of SCCmec cassettes in Staphylococcus aureus assemblies.",
          "url": "https://bactopia.github.io/bactopia-tools/sccmec",
          "path": "/bactopia-tools/sccmec",
          "tags": [
            "resistance",
            "staphylococcus-aureus",
            "mrsa",
            "sccmec",
            "typing",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/sccmec.mdx"
        },
        {
          "title": "scrubber",
          "description": "Removal of human and contaminant sequences from metagenomic reads.",
          "url": "https://bactopia.github.io/bactopia-tools/scrubber",
          "path": "/bactopia-tools/scrubber",
          "tags": [
            "metagenomics",
            "decontamination",
            "human-removal",
            "read-filtering",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/scrubber.mdx"
        },
        {
          "title": "seqsero2",
          "description": "Salmonella serotype prediction from sequencing reads or assemblies.",
          "url": "https://bactopia.github.io/bactopia-tools/seqsero2",
          "path": "/bactopia-tools/seqsero2",
          "tags": [
            "salmonella",
            "serotyping",
            "epidemiology",
            "o-antigen",
            "h-antigen",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/seqsero2.mdx"
        },
        {
          "title": "seroba",
          "description": "Serotyping of Streptococcus pneumoniae from Illumina paired-end reads.",
          "url": "https://bactopia.github.io/bactopia-tools/seroba",
          "path": "/bactopia-tools/seroba",
          "tags": [
            "serotyping",
            "streptococcus-pneumoniae",
            "capsule",
            "cps-locus",
            "vaccine",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/seroba.mdx"
        },
        {
          "title": "shigapass",
          "description": "Prediction of Shigella serotypes and differentiation from EIEC.",
          "url": "https://bactopia.github.io/bactopia-tools/shigapass",
          "path": "/bactopia-tools/shigapass",
          "tags": [
            "shigella",
            "eiec",
            "serotyping",
            "o-antigen",
            "ipa-genes",
            "epidemiology",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/shigapass.mdx"
        },
        {
          "title": "shigatyper",
          "description": "Rapid determination of Shigella serotypes from sequencing reads.",
          "url": "https://bactopia.github.io/bactopia-tools/shigatyper",
          "path": "/bactopia-tools/shigatyper",
          "tags": [
            "shigella",
            "serotyping",
            "k-mer",
            "illumina",
            "nanopore",
            "epidemiology",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/shigatyper.mdx"
        },
        {
          "title": "shigeifinder",
          "description": "In silico serotype prediction for Shigella and Enteroinvasive E. coli (EIEC).",
          "url": "https://bactopia.github.io/bactopia-tools/shigeifinder",
          "path": "/bactopia-tools/shigeifinder",
          "tags": [
            "shigella",
            "eiec",
            "serotyping",
            "prediction",
            "epidemiology",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/shigeifinder.mdx"
        },
        {
          "title": "sistr",
          "description": "Serovar prediction of Salmonella enterica from assemblies.",
          "url": "https://bactopia.github.io/bactopia-tools/sistr",
          "path": "/bactopia-tools/sistr",
          "tags": [
            "salmonella",
            "serovar",
            "cgmlst",
            "typing",
            "sistr",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/sistr.mdx"
        },
        {
          "title": "snippy",
          "description": "Rapid haplotype variant calling and core genome alignment.",
          "url": "https://bactopia.github.io/bactopia-tools/snippy",
          "path": "/bactopia-tools/snippy",
          "tags": [
            "snp",
            "variant-calling",
            "phylogeny",
            "core-genome",
            "snippy",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/snippy.mdx"
        },
        {
          "title": "spatyper",
          "description": "spa typing of Staphylococcus aureus assemblies.",
          "url": "https://bactopia.github.io/bactopia-tools/spatyper",
          "path": "/bactopia-tools/spatyper",
          "tags": [
            "staphylococcus-aureus",
            "spa-typing",
            "epidemiology",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/spatyper.mdx"
        },
        {
          "title": "ssuissero",
          "description": "Serotype prediction of Streptococcus suis assemblies.",
          "url": "https://bactopia.github.io/bactopia-tools/ssuissero",
          "path": "/bactopia-tools/ssuissero",
          "tags": [
            "streptococcus-suis",
            "serotyping",
            "fasta",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/ssuissero.mdx"
        },
        {
          "title": "staphtyper",
          "description": "Comprehensive typing of Staphylococcus aureus genomes.",
          "url": "https://bactopia.github.io/bactopia-tools/staphtyper",
          "path": "/bactopia-tools/staphtyper",
          "tags": [
            "staphylococcus-aureus",
            "agr",
            "spa",
            "sccmec",
            "typing",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/staphtyper.mdx"
        },
        {
          "title": "stecfinder",
          "description": "Serotype identification of Shiga toxin-producing E. coli.",
          "url": "https://bactopia.github.io/bactopia-tools/stecfinder",
          "path": "/bactopia-tools/stecfinder",
          "tags": [
            "stec",
            "serotype",
            "e-coli",
            "shiga-toxin",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/stecfinder.mdx"
        },
        {
          "title": "sylph",
          "description": "Taxonomic profiling by abundance-corrected MinHash.",
          "url": "https://bactopia.github.io/bactopia-tools/sylph",
          "path": "/bactopia-tools/sylph",
          "tags": [
            "taxonomic-profiling",
            "metagenomics",
            "minhash",
            "abundance",
            "sylph",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/sylph.mdx"
        },
        {
          "title": "tblastn",
          "description": "Search against translated nucleotide databases using protein queries.",
          "url": "https://bactopia.github.io/bactopia-tools/tblastn",
          "path": "/bactopia-tools/tblastn",
          "tags": [
            "fasta",
            "blast",
            "alignment",
            "protein",
            "nucleotide",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/tblastn.mdx"
        },
        {
          "title": "tblastx",
          "description": "Search against translated nucleotide databases using translated nucleotide queries.",
          "url": "https://bactopia.github.io/bactopia-tools/tblastx",
          "path": "/bactopia-tools/tblastx",
          "tags": [
            "fasta",
            "blast",
            "alignment",
            "protein",
            "translation",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/tblastx.mdx"
        },
        {
          "title": "tbprofiler",
          "description": "Detection of antimicrobial resistance and lineage typing of Mycobacterium tuberculosis.",
          "url": "https://bactopia.github.io/bactopia-tools/tbprofiler",
          "path": "/bactopia-tools/tbprofiler",
          "tags": [
            "mycobacterium-tuberculosis",
            "resistance",
            "lineage",
            "typing",
            "tb",
            "bactopia-tool"
          ],
          "source_file": "bactopia-tools/tbprofiler.mdx"
        }
      ]
    },
    {
      "key": "bactopia-pipelines",
      "title": "Bactopia Pipelines",
      "route_base": "/bactopia-pipelines",
      "description": "Complete analysis pipelines built from Bactopia's subworkflows and modules.",
      "page_count": 4,
      "pages": [
        {
          "title": "Bactopia Pipelines",
          "description": "Bactopia analysis pipelines",
          "url": "https://bactopia.github.io/bactopia-pipelines",
          "path": "/bactopia-pipelines",
          "tags": [],
          "source_file": "bactopia-pipelines/index.mdx",
          "sidebar_position": 1
        },
        {
          "title": "cleanyerreads",
          "description": "Quality control and optional host read removal from raw sequencing reads.",
          "url": "https://bactopia.github.io/bactopia-pipelines/cleanyerreads",
          "path": "/bactopia-pipelines/cleanyerreads",
          "tags": [
            "reads",
            "quality-control",
            "trimming",
            "filtering",
            "host-removal",
            "preprocessing",
            "named-workflow"
          ],
          "source_file": "bactopia-pipelines/cleanyerreads.mdx"
        },
        {
          "title": "staphopia",
          "description": "Comprehensive analysis pipeline for Staphylococcus aureus isolates.",
          "url": "https://bactopia.github.io/bactopia-pipelines/staphopia",
          "path": "/bactopia-pipelines/staphopia",
          "tags": [
            "staphylococcus-aureus",
            "assembly",
            "annotation",
            "amr",
            "mlst",
            "spa-typing",
            "agr-typing",
            "sccmec",
            "named-workflow"
          ],
          "source_file": "bactopia-pipelines/staphopia.mdx"
        },
        {
          "title": "teton",
          "description": "Taxonomic classification and abundance profiling of metagenomic reads.",
          "url": "https://bactopia.github.io/bactopia-pipelines/teton",
          "path": "/bactopia-pipelines/teton",
          "tags": [
            "metagenomics",
            "classification",
            "kraken2",
            "bracken",
            "abundance",
            "profiling",
            "named-workflow"
          ],
          "source_file": "bactopia-pipelines/teton.mdx"
        }
      ]
    },
    {
      "key": "developers",
      "title": "Developers",
      "route_base": "/developers",
      "description": "Developer reference for CLI commands, subworkflows, modules, and AI skills.",
      "page_count": 221,
      "pages": [
        {
          "title": "Developers",
          "description": "Bactopia developer reference for CLI commands, subworkflows, and modules",
          "url": "https://bactopia.github.io/developers",
          "path": "/developers",
          "tags": [],
          "source_file": "developers/index.mdx"
        },
        {
          "title": "abricate",
          "description": "Mass screening of contigs for antimicrobial and virulence genes.",
          "url": "https://bactopia.github.io/developers/subworkflows/abricate",
          "path": "/developers/subworkflows/abricate",
          "tags": [
            "bacteria",
            "assembly",
            "antimicrobial-resistance",
            "virulence",
            "workflow",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/abricate.mdx"
        },
        {
          "title": "abricate_run",
          "description": "Mass screening of contigs for antimicrobial and virulence genes.",
          "url": "https://bactopia.github.io/developers/modules/abricate_run",
          "path": "/developers/modules/abricate_run",
          "tags": [
            "bacteria",
            "assembly",
            "fasta",
            "antimicrobial-resistance",
            "virulence",
            "plasmid",
            "mobile-genetic-elements",
            "sample-scope"
          ],
          "source_file": "developers/modules/abricate_run.mdx"
        },
        {
          "title": "abricate_summary",
          "description": "Summarize Abricate screening results.",
          "url": "https://bactopia.github.io/developers/modules/abricate_summary",
          "path": "/developers/modules/abricate_summary",
          "tags": [
            "bacteria",
            "tab-delimited",
            "antimicrobial-resistance",
            "run-scope"
          ],
          "source_file": "developers/modules/abricate_summary.mdx"
        },
        {
          "title": "abritamr",
          "description": "Identify antimicrobial resistance genes using AMRFinderPlus.",
          "url": "https://bactopia.github.io/developers/subworkflows/abritamr",
          "path": "/developers/subworkflows/abritamr",
          "tags": [
            "bacteria",
            "antimicrobial-resistance",
            "amr",
            "amrfinderplus",
            "classification",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/abritamr.mdx"
        },
        {
          "title": "abritamr_run",
          "description": "Detect antimicrobial resistance and virulence genes.",
          "url": "https://bactopia.github.io/developers/modules/abritamr_run",
          "path": "/developers/modules/abritamr_run",
          "tags": [
            "bacteria",
            "assembly",
            "fasta",
            "antimicrobial-resistance",
            "nata",
            "amrfinderplus",
            "sample-scope"
          ],
          "source_file": "developers/modules/abritamr_run.mdx"
        },
        {
          "title": "agrvate",
          "description": "Determine the agr locus type and operon variants in Staphylococcus aureus.",
          "url": "https://bactopia.github.io/developers/modules/agrvate",
          "path": "/developers/modules/agrvate",
          "tags": [
            "bacteria",
            "assembly",
            "fasta",
            "typing",
            "virulence",
            "staphylococcus",
            "aureus",
            "agr",
            "sample-scope"
          ],
          "source_file": "developers/modules/agrvate.mdx"
        },
        {
          "title": "agrvate",
          "description": "Identify Staphylococcus aureus agr locus type and operon variants.",
          "url": "https://bactopia.github.io/developers/subworkflows/agrvate",
          "path": "/developers/subworkflows/agrvate",
          "tags": [
            "staphylococcus-aureus",
            "assembly",
            "agr-locus",
            "virulence",
            "quorum-sensing",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/agrvate.mdx"
        },
        {
          "title": "AI Skills",
          "description": "Reference for AI skills that automate Bactopia development tasks",
          "url": "https://bactopia.github.io/developers/ai-skills",
          "path": "/developers/ai-skills",
          "tags": [],
          "source_file": "developers/ai-skills/index.mdx"
        },
        {
          "title": "amrfinderplus",
          "description": "Find antimicrobial resistance genes and point mutations.",
          "url": "https://bactopia.github.io/developers/subworkflows/amrfinderplus",
          "path": "/developers/subworkflows/amrfinderplus",
          "tags": [
            "bacteria",
            "assembly",
            "antimicrobial-resistance",
            "gene-prediction",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/amrfinderplus.mdx"
        },
        {
          "title": "amrfinderplus_run",
          "description": "Identify antimicrobial resistance and virulence genes in gene or protein sequences.",
          "url": "https://bactopia.github.io/developers/modules/amrfinderplus_run",
          "path": "/developers/modules/amrfinderplus_run",
          "tags": [
            "bacteria",
            "fasta",
            "antimicrobial-resistance",
            "virulence",
            "ncbi",
            "amr",
            "genes",
            "proteins",
            "sample-scope"
          ],
          "source_file": "developers/modules/amrfinderplus_run.mdx"
        },
        {
          "title": "amrfinderplus_update",
          "description": "Download and index the latest AMRFinder+ database.",
          "url": "https://bactopia.github.io/developers/modules/amrfinderplus_update",
          "path": "/developers/modules/amrfinderplus_update",
          "tags": [
            "bacteria",
            "database",
            "antimicrobial-resistance",
            "update",
            "download",
            "ncbi",
            "sample-scope"
          ],
          "source_file": "developers/modules/amrfinderplus_update.mdx"
        },
        {
          "title": "ariba",
          "description": "Rapidly identify genes by creating local assemblies from paired-end reads.",
          "url": "https://bactopia.github.io/developers/subworkflows/ariba",
          "path": "/developers/subworkflows/ariba",
          "tags": [
            "bacteria",
            "reads",
            "antimicrobial-resistance",
            "virulence",
            "local-assembly",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/ariba.mdx"
        },
        {
          "title": "ariba_getref",
          "description": "Download and prepare reference databases for ARIBA analysis.",
          "url": "https://bactopia.github.io/developers/modules/ariba_getref",
          "path": "/developers/modules/ariba_getref",
          "tags": [
            "bacteria",
            "database",
            "download",
            "antimicrobial-resistance",
            "virulence",
            "ariba",
            "setup",
            "run-scope"
          ],
          "source_file": "developers/modules/ariba_getref.mdx"
        },
        {
          "title": "ariba_run",
          "description": "Identify genes by local assembly of reads.",
          "url": "https://bactopia.github.io/developers/modules/ariba_run",
          "path": "/developers/modules/ariba_run",
          "tags": [
            "fastq",
            "local-assembly",
            "antimicrobial-resistance",
            "virulence",
            "ariba",
            "sample-scope"
          ],
          "source_file": "developers/modules/ariba_run.mdx"
        },
        {
          "title": "bactopia-atb-downloader",
          "description": "Download All-the-Bacteria assemblies based on input query",
          "url": "https://bactopia.github.io/developers/cli/bactopia-atb-downloader",
          "path": "/developers/cli/bactopia-atb-downloader",
          "tags": [],
          "source_file": "developers/cli/bactopia-atb-downloader.mdx"
        },
        {
          "title": "bactopia-atb-formatter",
          "description": "Restructure All-the-Bacteria assemblies to allow usage with Bactopia Tools",
          "url": "https://bactopia.github.io/developers/cli/bactopia-atb-formatter",
          "path": "/developers/cli/bactopia-atb-formatter",
          "tags": [],
          "source_file": "developers/cli/bactopia-atb-formatter.mdx"
        },
        {
          "title": "bactopia-bracken-to-excel",
          "description": "Write Bracken abundances to an Excel file.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-bracken-to-excel",
          "path": "/developers/cli/bactopia-bracken-to-excel",
          "tags": [],
          "source_file": "developers/cli/bactopia-bracken-to-excel.mdx"
        },
        {
          "title": "bactopia-catalog",
          "description": "Generate machine-readable catalog of all Bactopia components.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-catalog",
          "path": "/developers/cli/bactopia-catalog",
          "tags": [],
          "source_file": "developers/cli/bactopia-catalog.mdx"
        },
        {
          "title": "bactopia-check-assembly-accession",
          "description": "Verify NCBI Assembly accession is latest and still available.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-check-assembly-accession",
          "path": "/developers/cli/bactopia-check-assembly-accession",
          "tags": [],
          "source_file": "developers/cli/bactopia-check-assembly-accession.mdx"
        },
        {
          "title": "bactopia-check-fastqs",
          "description": "Verify input FASTQs meet minimum requirements.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-check-fastqs",
          "path": "/developers/cli/bactopia-check-fastqs",
          "tags": [],
          "source_file": "developers/cli/bactopia-check-fastqs.mdx"
        },
        {
          "title": "bactopia-citations",
          "description": "Print or validate citations used throughout Bactopia.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-citations",
          "path": "/developers/cli/bactopia-citations",
          "tags": [],
          "source_file": "developers/cli/bactopia-citations.mdx"
        },
        {
          "title": "bactopia-cleanup-coverage",
          "description": "Reduce redundancy in per-base coverage from genomeCoverageBed output.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-cleanup-coverage",
          "path": "/developers/cli/bactopia-cleanup-coverage",
          "tags": [],
          "source_file": "developers/cli/bactopia-cleanup-coverage.mdx"
        },
        {
          "title": "bactopia-datasets",
          "description": "Download optional datasets to supplement your analyses with Bactopia",
          "url": "https://bactopia.github.io/developers/cli/bactopia-datasets",
          "path": "/developers/cli/bactopia-datasets",
          "tags": [],
          "source_file": "developers/cli/bactopia-datasets.mdx"
        },
        {
          "title": "bactopia-docs",
          "description": "Validate reference-doc staleness across a Bactopia repo.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-docs",
          "path": "/developers/cli/bactopia-docs",
          "tags": [],
          "source_file": "developers/cli/bactopia-docs.mdx"
        },
        {
          "title": "bactopia-download",
          "description": "Builds Bactopia environments for use with Nextflow.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-download",
          "path": "/developers/cli/bactopia-download",
          "tags": [],
          "source_file": "developers/cli/bactopia-download.mdx"
        },
        {
          "title": "bactopia-kraken-bracken-summary",
          "description": "Update the Bracken abundances with unclassified counts.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-kraken-bracken-summary",
          "path": "/developers/cli/bactopia-kraken-bracken-summary",
          "tags": [],
          "source_file": "developers/cli/bactopia-kraken-bracken-summary.mdx"
        },
        {
          "title": "bactopia-lint",
          "description": "Lint Bactopia pipeline components against style guidelines.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-lint",
          "path": "/developers/cli/bactopia-lint",
          "tags": [],
          "source_file": "developers/cli/bactopia-lint.mdx"
        },
        {
          "title": "bactopia-mask-consensus",
          "description": "Snippy consensus (subs) with coverage masking.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-mask-consensus",
          "path": "/developers/cli/bactopia-mask-consensus",
          "tags": [],
          "source_file": "developers/cli/bactopia-mask-consensus.mdx"
        },
        {
          "title": "bactopia-merge-schemas",
          "description": "Builds a Nextflow Schema and/or Nextflow config for a given workflow.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-merge-schemas",
          "path": "/developers/cli/bactopia-merge-schemas",
          "tags": [],
          "source_file": "developers/cli/bactopia-merge-schemas.mdx"
        },
        {
          "title": "bactopia-prepare",
          "description": "Create a 'file of filenames' (FOFN) of samples to be processed by Bactopia",
          "url": "https://bactopia.github.io/developers/cli/bactopia-prepare",
          "path": "/developers/cli/bactopia-prepare",
          "tags": [],
          "source_file": "developers/cli/bactopia-prepare.mdx"
        },
        {
          "title": "bactopia-prune",
          "description": "Removes stale Bactopia environments that no longer match current module versions.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-prune",
          "path": "/developers/cli/bactopia-prune",
          "tags": [],
          "source_file": "developers/cli/bactopia-prune.mdx"
        },
        {
          "title": "bactopia-pubmlst-build",
          "description": "Build PubMLST databases for use with the 'mlst' Bactopia Tool.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-pubmlst-build",
          "path": "/developers/cli/bactopia-pubmlst-build",
          "tags": [],
          "source_file": "developers/cli/bactopia-pubmlst-build.mdx"
        },
        {
          "title": "bactopia-pubmlst-setup",
          "description": "One-time setup for interacting with the PubMLST API",
          "url": "https://bactopia.github.io/developers/cli/bactopia-pubmlst-setup",
          "path": "/developers/cli/bactopia-pubmlst-setup",
          "tags": [],
          "source_file": "developers/cli/bactopia-pubmlst-setup.mdx"
        },
        {
          "title": "bactopia-review-tests",
          "description": "Review nf-test results with grouped error analysis and timing checks.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-review-tests",
          "path": "/developers/cli/bactopia-review-tests",
          "tags": [],
          "source_file": "developers/cli/bactopia-review-tests.mdx"
        },
        {
          "title": "bactopia-scaffold",
          "description": "Scaffold Bactopia components from bioconda/conda-forge packages.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-scaffold",
          "path": "/developers/cli/bactopia-scaffold",
          "tags": [],
          "source_file": "developers/cli/bactopia-scaffold.mdx"
        },
        {
          "title": "bactopia-scrubber-summary",
          "description": "Create a before-and-after report from human read scrubbing.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-scrubber-summary",
          "path": "/developers/cli/bactopia-scrubber-summary",
          "tags": [],
          "source_file": "developers/cli/bactopia-scrubber-summary.mdx"
        },
        {
          "title": "bactopia-search",
          "description": "Query against ENA and SRA for public accessions to process with Bactopia",
          "url": "https://bactopia.github.io/developers/cli/bactopia-search",
          "path": "/developers/cli/bactopia-search",
          "tags": [],
          "source_file": "developers/cli/bactopia-search.mdx"
        },
        {
          "title": "bactopia-status",
          "description": "Show a snapshot of the Bactopia project state.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-status",
          "path": "/developers/cli/bactopia-status",
          "tags": [],
          "source_file": "developers/cli/bactopia-status.mdx"
        },
        {
          "title": "bactopia-summary",
          "description": "Generate a summary table from the Bactopia results.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-summary",
          "path": "/developers/cli/bactopia-summary",
          "tags": [],
          "source_file": "developers/cli/bactopia-summary.mdx"
        },
        {
          "title": "bactopia-sysinfo",
          "description": "Auto-detect host RAM and CPUs, emit Nextflow CLI fragments for local profiles.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-sysinfo",
          "path": "/developers/cli/bactopia-sysinfo",
          "tags": [],
          "source_file": "developers/cli/bactopia-sysinfo.mdx"
        },
        {
          "title": "bactopia-test",
          "description": "Run nf-test suites for Bactopia components.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-test",
          "path": "/developers/cli/bactopia-test",
          "tags": [],
          "source_file": "developers/cli/bactopia-test.mdx"
        },
        {
          "title": "bactopia-teton-prepare",
          "description": "Prepare sample sheets for downstream analysis in the Teton workflow.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-teton-prepare",
          "path": "/developers/cli/bactopia-teton-prepare",
          "tags": [],
          "source_file": "developers/cli/bactopia-teton-prepare.mdx"
        },
        {
          "title": "bactopia-update",
          "description": "Check if modules used by Bactopia Tools have newer versions available",
          "url": "https://bactopia.github.io/developers/cli/bactopia-update",
          "path": "/developers/cli/bactopia-update",
          "tags": [],
          "source_file": "developers/cli/bactopia-update.mdx"
        },
        {
          "title": "bactopia-workflows",
          "description": "Output the path to a Bactopia workflow main.nf file.",
          "url": "https://bactopia.github.io/developers/cli/bactopia-workflows",
          "path": "/developers/cli/bactopia-workflows",
          "tags": [],
          "source_file": "developers/cli/bactopia-workflows.mdx"
        },
        {
          "title": "bactopia_assembler",
          "description": "Assemble bacterial genomes using short read, long read, or hybrid strategies.",
          "url": "https://bactopia.github.io/developers/modules/bactopia_assembler",
          "path": "/developers/modules/bactopia_assembler",
          "tags": [
            "bacteria",
            "assembly",
            "hybrid",
            "shovill",
            "dragonflye",
            "unicycler",
            "illumina",
            "nanopore",
            "sample-scope"
          ],
          "source_file": "developers/modules/bactopia_assembler.mdx"
        },
        {
          "title": "bactopia_assembler",
          "description": "Assemble bacterial genomes using automated assembler selection.",
          "url": "https://bactopia.github.io/developers/subworkflows/bactopia_assembler",
          "path": "/developers/subworkflows/bactopia_assembler",
          "tags": [
            "bacteria",
            "assembly",
            "hybrid",
            "shovill",
            "dragonflye",
            "unicycler",
            "illumina",
            "nanopore",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/bactopia_assembler.mdx"
        },
        {
          "title": "bactopia_datasets",
          "description": "Download pre-compiled datasets required by Bactopia.",
          "url": "https://bactopia.github.io/developers/modules/bactopia_datasets",
          "path": "/developers/modules/bactopia_datasets",
          "tags": [
            "download",
            "database",
            "setup",
            "amr",
            "mlst",
            "minhash",
            "sourmash",
            "gtdb",
            "run-scope"
          ],
          "source_file": "developers/modules/bactopia_datasets.mdx"
        },
        {
          "title": "bactopia_datasets",
          "description": "Download and provide pre-compiled datasets required by Bactopia.",
          "url": "https://bactopia.github.io/developers/subworkflows/bactopia_datasets",
          "path": "/developers/subworkflows/bactopia_datasets",
          "tags": [
            "download",
            "database",
            "setup",
            "amr",
            "mlst",
            "minhash",
            "sourmash",
            "gtdb",
            "custom-scope"
          ],
          "source_file": "developers/subworkflows/bactopia_datasets.mdx"
        },
        {
          "title": "bactopia_gather",
          "description": "Search, validate, gather, or simulate input samples.",
          "url": "https://bactopia.github.io/developers/modules/bactopia_gather",
          "path": "/developers/modules/bactopia_gather",
          "tags": [
            "fastq",
            "validation",
            "sra",
            "ena",
            "download",
            "merging",
            "simulation",
            "art",
            "ncbi",
            "sample-scope"
          ],
          "source_file": "developers/modules/bactopia_gather.mdx"
        },
        {
          "title": "bactopia_gather",
          "description": "Search, validate, gather, and standardize input samples.",
          "url": "https://bactopia.github.io/developers/subworkflows/bactopia_gather",
          "path": "/developers/subworkflows/bactopia_gather",
          "tags": [
            "validation",
            "download",
            "merging",
            "simulation",
            "metadata",
            "fastq",
            "sra",
            "ena",
            "art",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/bactopia_gather.mdx"
        },
        {
          "title": "bactopia_qc",
          "description": "Automated quality control, error correction, and read subsampling.",
          "url": "https://bactopia.github.io/developers/modules/bactopia_qc",
          "path": "/developers/modules/bactopia_qc",
          "tags": [
            "fastq",
            "qc",
            "adapter-removal",
            "error-correction",
            "subsampling",
            "fastp",
            "bbduk",
            "lighter",
            "porechop",
            "nanoq",
            "fastqc",
            "nanoplot",
            "sample-scope"
          ],
          "source_file": "developers/modules/bactopia_qc.mdx"
        },
        {
          "title": "bactopia_qc",
          "description": "Perform comprehensive quality control on sequencing reads.",
          "url": "https://bactopia.github.io/developers/subworkflows/bactopia_qc",
          "path": "/developers/subworkflows/bactopia_qc",
          "tags": [
            "quality-control",
            "adapters",
            "error-correction",
            "subsampling",
            "fastq",
            "illumina",
            "nanopore",
            "fastp",
            "bbduk",
            "nanoq",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/bactopia_qc.mdx"
        },
        {
          "title": "bactopia_sketcher",
          "description": "Create genomic sketches and perform rapid taxonomic classification.",
          "url": "https://bactopia.github.io/developers/modules/bactopia_sketcher",
          "path": "/developers/modules/bactopia_sketcher",
          "tags": [
            "bacteria",
            "taxonomy",
            "classification",
            "minhash",
            "sketch",
            "mash",
            "sourmash",
            "refseq",
            "gtdb",
            "sample-scope"
          ],
          "source_file": "developers/modules/bactopia_sketcher.mdx"
        },
        {
          "title": "bactopia_sketcher",
          "description": "Create genomic sketches and perform rapid taxonomic classification.",
          "url": "https://bactopia.github.io/developers/subworkflows/bactopia_sketcher",
          "path": "/developers/subworkflows/bactopia_sketcher",
          "tags": [
            "taxonomy",
            "classification",
            "minhash",
            "sketch",
            "mash",
            "sourmash",
            "refseq",
            "gtdb",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/bactopia_sketcher.mdx"
        },
        {
          "title": "bactopia_teton",
          "description": "Predict genome size and route samples based on taxonomic classification.",
          "url": "https://bactopia.github.io/developers/modules/bactopia_teton",
          "path": "/developers/modules/bactopia_teton",
          "tags": [
            "taxonomy",
            "genome-size",
            "routing",
            "filtering",
            "bacteria",
            "sizemeup",
            "bracken",
            "sample-scope"
          ],
          "source_file": "developers/modules/bactopia_teton.mdx"
        },
        {
          "title": "bakta",
          "description": "Rapid bacterial genome annotation.",
          "url": "https://bactopia.github.io/developers/subworkflows/bakta",
          "path": "/developers/subworkflows/bakta",
          "tags": [
            "bacteria",
            "annotation",
            "genome",
            "functional-annotation",
            "taxonomy",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/bakta.mdx"
        },
        {
          "title": "bakta_download",
          "description": "Download the Bakta annotation database.",
          "url": "https://bactopia.github.io/developers/modules/bakta_download",
          "path": "/developers/modules/bakta_download",
          "tags": [
            "bacteria",
            "database",
            "download",
            "annotation",
            "bakta",
            "setup",
            "run-scope"
          ],
          "source_file": "developers/modules/bakta_download.mdx"
        },
        {
          "title": "bakta_run",
          "description": "Rapid and standardized annotation of bacterial genomes and plasmids.",
          "url": "https://bactopia.github.io/developers/modules/bakta_run",
          "path": "/developers/modules/bakta_run",
          "tags": [
            "bacteria",
            "annotation",
            "genome",
            "assembly",
            "prodigal",
            "compliant",
            "genbank",
            "ena",
            "sample-scope"
          ],
          "source_file": "developers/modules/bakta_run.mdx"
        },
        {
          "title": "blast_blastn",
          "description": "Search a nucleotide database using a nucleotide query.",
          "url": "https://bactopia.github.io/developers/modules/blast_blastn",
          "path": "/developers/modules/blast_blastn",
          "tags": [
            "blast",
            "blastn",
            "alignment",
            "dna",
            "search",
            "fasta",
            "sample-scope"
          ],
          "source_file": "developers/modules/blast_blastn.mdx"
        },
        {
          "title": "blast_blastp",
          "description": "Search a protein database using a protein query.",
          "url": "https://bactopia.github.io/developers/modules/blast_blastp",
          "path": "/developers/modules/blast_blastp",
          "tags": [
            "blast",
            "blastp",
            "alignment",
            "protein",
            "amino-acid",
            "search",
            "fasta",
            "sample-scope"
          ],
          "source_file": "developers/modules/blast_blastp.mdx"
        },
        {
          "title": "blast_blastx",
          "description": "Search a protein database using a translated nucleotide query.",
          "url": "https://bactopia.github.io/developers/modules/blast_blastx",
          "path": "/developers/modules/blast_blastx",
          "tags": [
            "blast",
            "blastx",
            "alignment",
            "translation",
            "protein",
            "dna",
            "search",
            "fasta",
            "sample-scope"
          ],
          "source_file": "developers/modules/blast_blastx.mdx"
        },
        {
          "title": "blast_tblastn",
          "description": "Search a translated nucleotide database using a protein query.",
          "url": "https://bactopia.github.io/developers/modules/blast_tblastn",
          "path": "/developers/modules/blast_tblastn",
          "tags": [
            "blast",
            "tblastn",
            "alignment",
            "translation",
            "protein",
            "dna",
            "search",
            "fasta",
            "sample-scope"
          ],
          "source_file": "developers/modules/blast_tblastn.mdx"
        },
        {
          "title": "blast_tblastx",
          "description": "Search a translated nucleotide database using a translated nucleotide query.",
          "url": "https://bactopia.github.io/developers/modules/blast_tblastx",
          "path": "/developers/modules/blast_tblastx",
          "tags": [
            "blast",
            "tblastx",
            "alignment",
            "translation",
            "dna",
            "search",
            "fasta",
            "sample-scope"
          ],
          "source_file": "developers/modules/blast_tblastx.mdx"
        },
        {
          "title": "blastn",
          "description": "Search a nucleotide database using nucleotide query sequences.",
          "url": "https://bactopia.github.io/developers/subworkflows/blastn",
          "path": "/developers/subworkflows/blastn",
          "tags": [
            "blast",
            "alignment",
            "nucleotide",
            "search",
            "fasta",
            "database",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/blastn.mdx"
        },
        {
          "title": "blastp",
          "description": "Search protein sequences against protein database.",
          "url": "https://bactopia.github.io/developers/subworkflows/blastp",
          "path": "/developers/subworkflows/blastp",
          "tags": [
            "blast",
            "protein",
            "alignment",
            "database",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/blastp.mdx"
        },
        {
          "title": "blastx",
          "description": "Translate nucleotide sequences and search protein database.",
          "url": "https://bactopia.github.io/developers/subworkflows/blastx",
          "path": "/developers/subworkflows/blastx",
          "tags": [
            "blast",
            "protein",
            "translation",
            "alignment",
            "database",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/blastx.mdx"
        },
        {
          "title": "bracken",
          "description": "Taxonomic classification and abundance estimation.",
          "url": "https://bactopia.github.io/developers/modules/bracken",
          "path": "/developers/modules/bracken",
          "tags": [
            "metagenomics",
            "classification",
            "taxonomy",
            "abundance",
            "kraken2",
            "bracken",
            "krona",
            "sample-scope"
          ],
          "source_file": "developers/modules/bracken.mdx"
        },
        {
          "title": "bracken",
          "description": "Estimate species abundance from metagenomic reads.",
          "url": "https://bactopia.github.io/developers/subworkflows/bracken",
          "path": "/developers/subworkflows/bracken",
          "tags": [
            "metagenomics",
            "taxonomic-classification",
            "abundance-estimation",
            "kraken2",
            "bracken",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/bracken.mdx"
        },
        {
          "title": "btyper3",
          "description": "In silico typing and characterization of *Bacillus cereus* group genomes.",
          "url": "https://bactopia.github.io/developers/modules/btyper3",
          "path": "/developers/modules/btyper3",
          "tags": [
            "bacteria",
            "bacillus",
            "cereus",
            "typing",
            "virulence",
            "toxin",
            "amr",
            "mlst",
            "sample-scope"
          ],
          "source_file": "developers/modules/btyper3.mdx"
        },
        {
          "title": "btyper3",
          "description": "In silico taxonomic classification of Bacillus cereus group genomes.",
          "url": "https://bactopia.github.io/developers/subworkflows/btyper3",
          "path": "/developers/subworkflows/btyper3",
          "tags": [
            "bacillus",
            "cereus",
            "taxonomy",
            "typing",
            "toxin-genes",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/btyper3.mdx"
        },
        {
          "title": "busco",
          "description": "Assess genome assembly completeness using single-copy orthologs.",
          "url": "https://bactopia.github.io/developers/modules/busco",
          "path": "/developers/modules/busco",
          "tags": [
            "quality-control",
            "completeness",
            "genome",
            "assembly",
            "orthologs",
            "busco",
            "sample-scope"
          ],
          "source_file": "developers/modules/busco.mdx"
        },
        {
          "title": "busco",
          "description": "Assess genome assembly completeness using BUSCO.",
          "url": "https://bactopia.github.io/developers/subworkflows/busco",
          "path": "/developers/subworkflows/busco",
          "tags": [
            "assembly",
            "completeness",
            "quality",
            "assessment",
            "orthologs",
            "evaluation",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/busco.mdx"
        },
        {
          "title": "checkm",
          "description": "Assess metagenome bin completeness using CheckM.",
          "url": "https://bactopia.github.io/developers/subworkflows/checkm",
          "path": "/developers/subworkflows/checkm",
          "tags": [
            "metagenome",
            "bin",
            "completeness",
            "contamination",
            "mag",
            "quality",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/checkm.mdx"
        },
        {
          "title": "checkm2",
          "description": "Assess metagenome bin completeness using CheckM2.",
          "url": "https://bactopia.github.io/developers/subworkflows/checkm2",
          "path": "/developers/subworkflows/checkm2",
          "tags": [
            "metagenome",
            "bin",
            "completeness",
            "contamination",
            "mag",
            "quality",
            "machine-learning",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/checkm2.mdx"
        },
        {
          "title": "checkm2_download",
          "description": "Download the pre-trained CheckM2 database.",
          "url": "https://bactopia.github.io/developers/modules/checkm2_download",
          "path": "/developers/modules/checkm2_download",
          "tags": [
            "checkm2",
            "download",
            "database",
            "diamond",
            "machine-learning",
            "sample-scope"
          ],
          "source_file": "developers/modules/checkm2_download.mdx"
        },
        {
          "title": "checkm2_predict",
          "description": "Assess genome quality using machine learning.",
          "url": "https://bactopia.github.io/developers/modules/checkm2_predict",
          "path": "/developers/modules/checkm2_predict",
          "tags": [
            "quality-control",
            "completeness",
            "contamination",
            "machine-learning",
            "bacteria",
            "archaea",
            "sample-scope"
          ],
          "source_file": "developers/modules/checkm2_predict.mdx"
        },
        {
          "title": "checkm_lineagewf",
          "description": "Assess genome quality using lineage-specific marker sets.",
          "url": "https://bactopia.github.io/developers/modules/checkm_lineagewf",
          "path": "/developers/modules/checkm_lineagewf",
          "tags": [
            "quality-control",
            "completeness",
            "contamination",
            "marker-genes",
            "lineage",
            "bacteria",
            "archaea",
            "sample-scope"
          ],
          "source_file": "developers/modules/checkm_lineagewf.mdx"
        },
        {
          "title": "clermontyping",
          "description": "Determine the phylogroup of Escherichia coli isolates.",
          "url": "https://bactopia.github.io/developers/modules/clermontyping",
          "path": "/developers/modules/clermontyping",
          "tags": [
            "bacteria",
            "escherichia-coli",
            "typing",
            "phylotyping",
            "pcr",
            "phylogroup",
            "sample-scope"
          ],
          "source_file": "developers/modules/clermontyping.mdx"
        },
        {
          "title": "clermontyping",
          "description": "Predict phylogroups of Escherichia coli from genome assemblies.",
          "url": "https://bactopia.github.io/developers/subworkflows/clermontyping",
          "path": "/developers/subworkflows/clermontyping",
          "tags": [
            "escherichia-coli",
            "phylogroup",
            "typing",
            "clermont",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/clermontyping.mdx"
        },
        {
          "title": "CLI Reference",
          "description": "Command-line reference for all bactopia-py CLI commands",
          "url": "https://bactopia.github.io/developers/cli",
          "path": "/developers/cli",
          "tags": [],
          "source_file": "developers/cli/index.mdx"
        },
        {
          "title": "clonalframeml",
          "description": "Inference of recombination in bacterial genomes.",
          "url": "https://bactopia.github.io/developers/modules/clonalframeml",
          "path": "/developers/modules/clonalframeml",
          "tags": [
            "bacteria",
            "recombination",
            "phylogeny",
            "alignment",
            "msa",
            "evolution",
            "run-scope"
          ],
          "source_file": "developers/modules/clonalframeml.mdx"
        },
        {
          "title": "clonalframeml",
          "description": "Detect and mask recombination events in bacterial phylogenies.",
          "url": "https://bactopia.github.io/developers/subworkflows/clonalframeml",
          "path": "/developers/subworkflows/clonalframeml",
          "tags": [
            "recombination",
            "phylogeny",
            "masking",
            "clonalframe",
            "bacterial-evolution",
            "run-scope"
          ],
          "source_file": "developers/subworkflows/clonalframeml.mdx"
        },
        {
          "title": "csvtk_concat",
          "description": "Concatenate multiple CSV or TSV files into a single table.",
          "url": "https://bactopia.github.io/developers/modules/csvtk_concat",
          "path": "/developers/modules/csvtk_concat",
          "tags": [
            "utility",
            "table",
            "merge",
            "concat",
            "csv",
            "tsv",
            "csvtk",
            "run-scope"
          ],
          "source_file": "developers/modules/csvtk_concat.mdx"
        },
        {
          "title": "csvtk_join",
          "description": "Join two CSV or TSV files based on common fields.",
          "url": "https://bactopia.github.io/developers/modules/csvtk_join",
          "path": "/developers/modules/csvtk_join",
          "tags": [
            "utility",
            "table",
            "join",
            "merge",
            "csv",
            "tsv",
            "csvtk",
            "relational",
            "run-scope"
          ],
          "source_file": "developers/modules/csvtk_join.mdx"
        },
        {
          "title": "defensefinder",
          "description": "Systematically search for anti-phage defense systems.",
          "url": "https://bactopia.github.io/developers/subworkflows/defensefinder",
          "path": "/developers/subworkflows/defensefinder",
          "tags": [
            "bacteria",
            "assembly",
            "anti-phage",
            "defense-systems",
            "immunity",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/defensefinder.mdx"
        },
        {
          "title": "defensefinder_run",
          "description": "Detect anti-phage defense systems using HMM profiles.",
          "url": "https://bactopia.github.io/developers/modules/defensefinder_run",
          "path": "/developers/modules/defensefinder_run",
          "tags": [
            "bacteria",
            "defense-systems",
            "antiviral",
            "phage",
            "crispr",
            "restriction-modification",
            "hmm",
            "macsyfinder",
            "sample-scope"
          ],
          "source_file": "developers/modules/defensefinder_run.mdx"
        },
        {
          "title": "defensefinder_update",
          "description": "Download and package the DefenseFinder and CasFinder model databases.",
          "url": "https://bactopia.github.io/developers/modules/defensefinder_update",
          "path": "/developers/modules/defensefinder_update",
          "tags": [
            "bacteria",
            "defense",
            "database",
            "download",
            "hmm",
            "casfinder",
            "crispr",
            "run-scope"
          ],
          "source_file": "developers/modules/defensefinder_update.mdx"
        },
        {
          "title": "ectyper",
          "description": "Predict *Escherichia coli* serotype (O and H antigens).",
          "url": "https://bactopia.github.io/developers/modules/ectyper",
          "path": "/developers/modules/ectyper",
          "tags": [
            "bacteria",
            "escherichia-coli",
            "serotype",
            "o-antigen",
            "h-antigen",
            "typing",
            "sample-scope"
          ],
          "source_file": "developers/modules/ectyper.mdx"
        },
        {
          "title": "ectyper",
          "description": "In silico prediction of Escherichia coli serotype.",
          "url": "https://bactopia.github.io/developers/subworkflows/ectyper",
          "path": "/developers/subworkflows/ectyper",
          "tags": [
            "escherichia",
            "coli",
            "serotype",
            "o-antigen",
            "h-antigen",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/ectyper.mdx"
        },
        {
          "title": "eggnog",
          "description": "Functional annotation through orthology assignment.",
          "url": "https://bactopia.github.io/developers/subworkflows/eggnog",
          "path": "/developers/subworkflows/eggnog",
          "tags": [
            "functional",
            "annotation",
            "orthology",
            "eggnog",
            "protein-domains",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/eggnog.mdx"
        },
        {
          "title": "eggnog_download",
          "description": "Download the eggNOG database for functional annotation.",
          "url": "https://bactopia.github.io/developers/modules/eggnog_download",
          "path": "/developers/modules/eggnog_download",
          "tags": [
            "eggnog",
            "database",
            "download",
            "annotation",
            "functional",
            "orthology",
            "sample-scope"
          ],
          "source_file": "developers/modules/eggnog_download.mdx"
        },
        {
          "title": "eggnog_mapper",
          "description": "Functional annotation of proteins using eggNOG orthology data.",
          "url": "https://bactopia.github.io/developers/modules/eggnog_mapper",
          "path": "/developers/modules/eggnog_mapper",
          "tags": [
            "functional-annotation",
            "orthology",
            "cog",
            "kegg",
            "go",
            "proteins",
            "eggnog",
            "sample-scope"
          ],
          "source_file": "developers/modules/eggnog_mapper.mdx"
        },
        {
          "title": "emmtyper",
          "description": "*emm*-typing of *Streptococcus pyogenes* (Group A Strep) assemblies.",
          "url": "https://bactopia.github.io/developers/modules/emmtyper",
          "path": "/developers/modules/emmtyper",
          "tags": [
            "bacteria",
            "streptococcus-pyogenes",
            "gas",
            "typing",
            "emm",
            "virulence",
            "m-protein",
            "sample-scope"
          ],
          "source_file": "developers/modules/emmtyper.mdx"
        },
        {
          "title": "emmtyper",
          "description": "Predict emm types of Streptococcus pyogenes from genome assemblies.",
          "url": "https://bactopia.github.io/developers/subworkflows/emmtyper",
          "path": "/developers/subworkflows/emmtyper",
          "tags": [
            "streptococcus-pyogenes",
            "emm-typing",
            "gas",
            "m-protein",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/emmtyper.mdx"
        },
        {
          "title": "fastani",
          "description": "Compute whole-genome Average Nucleotide Identity (ANI).",
          "url": "https://bactopia.github.io/developers/modules/fastani",
          "path": "/developers/modules/fastani",
          "tags": [
            "fastani",
            "ani",
            "average-nucleotide-identity",
            "taxonomy",
            "genomic-distance",
            "comparison",
            "run-scope"
          ],
          "source_file": "developers/modules/fastani.mdx"
        },
        {
          "title": "fastani",
          "description": "Calculate Average Nucleotide Identity (ANI) between genomes.",
          "url": "https://bactopia.github.io/developers/subworkflows/fastani",
          "path": "/developers/subworkflows/fastani",
          "tags": [
            "ani",
            "average-nucleotide-identity",
            "taxonomy",
            "species",
            "comparison",
            "run-scope"
          ],
          "source_file": "developers/subworkflows/fastani.mdx"
        },
        {
          "title": "gamma",
          "description": "Identification, classification, and annotation of translated gene matches.",
          "url": "https://bactopia.github.io/developers/modules/gamma",
          "path": "/developers/modules/gamma",
          "tags": [
            "gene-finding",
            "annotation",
            "homology",
            "alignment",
            "gamma",
            "psl",
            "sample-scope"
          ],
          "source_file": "developers/modules/gamma.mdx"
        },
        {
          "title": "gamma",
          "description": "Gene Allele Mutation Microbial Assessment.",
          "url": "https://bactopia.github.io/developers/subworkflows/gamma",
          "path": "/developers/subworkflows/gamma",
          "tags": [
            "gene",
            "allele",
            "mutation",
            "variant",
            "antimicrobial-resistance",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/gamma.mdx"
        },
        {
          "title": "genotyphi",
          "description": "Assign genotypes to Salmonella Typhi genomes.",
          "url": "https://bactopia.github.io/developers/subworkflows/genotyphi",
          "path": "/developers/subworkflows/genotyphi",
          "tags": [
            "salmonella",
            "typhi",
            "genotype",
            "antimicrobial-resistance",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/genotyphi.mdx"
        },
        {
          "title": "genotyphi_parse",
          "description": "Parse Mykrobe results to genotype *Salmonella* Typhi.",
          "url": "https://bactopia.github.io/developers/modules/genotyphi_parse",
          "path": "/developers/modules/genotyphi_parse",
          "tags": [
            "bacteria",
            "salmonella",
            "typhi",
            "genotyping",
            "mykrobe",
            "parser",
            "sample-scope"
          ],
          "source_file": "developers/modules/genotyphi_parse.mdx"
        },
        {
          "title": "gigatyper",
          "description": "Run all available MLST schemes for a species against an assembly",
          "url": "https://bactopia.github.io/developers/modules/gigatyper",
          "path": "/developers/modules/gigatyper",
          "tags": [
            "mlst",
            "typing",
            "multi-scheme",
            "sample-scope"
          ],
          "source_file": "developers/modules/gigatyper.mdx"
        },
        {
          "title": "gigatyper",
          "description": "Run all available MLST schemes for a species against an assembly",
          "url": "https://bactopia.github.io/developers/subworkflows/gigatyper",
          "path": "/developers/subworkflows/gigatyper",
          "tags": [
            "mlst",
            "typing",
            "multi-scheme",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/gigatyper.mdx"
        },
        {
          "title": "gtdb",
          "description": "Taxonomic classification with the Genome Taxonomy Database.",
          "url": "https://bactopia.github.io/developers/subworkflows/gtdb",
          "path": "/developers/subworkflows/gtdb",
          "tags": [
            "taxonomy",
            "classification",
            "gtdb",
            "phylogeny",
            "marker-genes",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/gtdb.mdx"
        },
        {
          "title": "gtdbtk_classifywf",
          "description": "Taxonomic classification of bacterial and archaeal genomes using GTDB-Tk.",
          "url": "https://bactopia.github.io/developers/modules/gtdbtk_classifywf",
          "path": "/developers/modules/gtdbtk_classifywf",
          "tags": [
            "taxonomy",
            "classification",
            "phylogeny",
            "gtdb",
            "bacteria",
            "archaea",
            "marker-genes",
            "sample-scope"
          ],
          "source_file": "developers/modules/gtdbtk_classifywf.mdx"
        },
        {
          "title": "gtdbtk_download",
          "description": "Download and configure the GTDB-Tk reference database.",
          "url": "https://bactopia.github.io/developers/modules/gtdbtk_download",
          "path": "/developers/modules/gtdbtk_download",
          "tags": [
            "gtdb",
            "taxonomy",
            "database",
            "download",
            "setup",
            "bacteria",
            "archaea",
            "sample-scope"
          ],
          "source_file": "developers/modules/gtdbtk_download.mdx"
        },
        {
          "title": "gubbins",
          "description": "Detect recombination and construct a recombination-free phylogeny.",
          "url": "https://bactopia.github.io/developers/modules/gubbins",
          "path": "/developers/modules/gubbins",
          "tags": [
            "bacteria",
            "recombination",
            "phylogeny",
            "alignment",
            "msa",
            "evolution",
            "snp",
            "run-scope"
          ],
          "source_file": "developers/modules/gubbins.mdx"
        },
        {
          "title": "gubbins",
          "description": "Detect and filter recombination regions in bacterial alignments.",
          "url": "https://bactopia.github.io/developers/subworkflows/gubbins",
          "path": "/developers/subworkflows/gubbins",
          "tags": [
            "recombination",
            "phylogeny",
            "filter",
            "snp",
            "core-genome",
            "run-scope"
          ],
          "source_file": "developers/subworkflows/gubbins.mdx"
        },
        {
          "title": "hicap",
          "description": "Predict *Haemophilus influenzae* capsule serotype.",
          "url": "https://bactopia.github.io/developers/modules/hicap",
          "path": "/developers/modules/hicap",
          "tags": [
            "bacteria",
            "haemophilus-influenzae",
            "serotype",
            "capsule",
            "typing",
            "nthi",
            "sample-scope"
          ],
          "source_file": "developers/modules/hicap.mdx"
        },
        {
          "title": "hicap",
          "description": "In silico serotyping of the Haemophilus influenzae capsule locus.",
          "url": "https://bactopia.github.io/developers/subworkflows/hicap",
          "path": "/developers/subworkflows/hicap",
          "tags": [
            "haemophilus",
            "influenzae",
            "serotype",
            "capsule",
            "cap-locus",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/hicap.mdx"
        },
        {
          "title": "hpsuissero",
          "description": "Predict *Haemophilus parasuis* serotype.",
          "url": "https://bactopia.github.io/developers/modules/hpsuissero",
          "path": "/developers/modules/hpsuissero",
          "tags": [
            "bacteria",
            "haemophilus-parasuis",
            "glaesserella-parasuis",
            "serotype",
            "typing",
            "capsule",
            "sample-scope"
          ],
          "source_file": "developers/modules/hpsuissero.mdx"
        },
        {
          "title": "hpsuissero",
          "description": "Rapid Haemophilus parasuis serotyping.",
          "url": "https://bactopia.github.io/developers/subworkflows/hpsuissero",
          "path": "/developers/subworkflows/hpsuissero",
          "tags": [
            "haemophilus",
            "parasuis",
            "serotype",
            "epidemiology",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/hpsuissero.mdx"
        },
        {
          "title": "iqtree",
          "description": "Efficient phylogenomic inference using Maximum Likelihood.",
          "url": "https://bactopia.github.io/developers/modules/iqtree",
          "path": "/developers/modules/iqtree",
          "tags": [
            "phylogeny",
            "tree",
            "maximum-likelihood",
            "bootstrap",
            "model-selection",
            "iqtree",
            "run-scope"
          ],
          "source_file": "developers/modules/iqtree.mdx"
        },
        {
          "title": "iqtree",
          "description": "Construct maximum likelihood phylogenetic trees from alignments.",
          "url": "https://bactopia.github.io/developers/subworkflows/iqtree",
          "path": "/developers/subworkflows/iqtree",
          "tags": [
            "phylogeny",
            "maximum-likelihood",
            "tree",
            "bootstrap",
            "model-selection",
            "run-scope"
          ],
          "source_file": "developers/subworkflows/iqtree.mdx"
        },
        {
          "title": "ismapper",
          "description": "Identify insertion sites and orientation of mobile genetic elements.",
          "url": "https://bactopia.github.io/developers/modules/ismapper",
          "path": "/developers/modules/ismapper",
          "tags": [
            "bacteria",
            "mobile-elements",
            "insertion-sequences",
            "mapping",
            "structural-variation",
            "ismapper",
            "sample-scope"
          ],
          "source_file": "developers/modules/ismapper.mdx"
        },
        {
          "title": "ismapper",
          "description": "Identify transposase insertion sites in bacterial genomes.",
          "url": "https://bactopia.github.io/developers/subworkflows/ismapper",
          "path": "/developers/subworkflows/ismapper",
          "tags": [
            "insertion",
            "sequence",
            "transposase",
            "mobile-genetic-elements",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/ismapper.mdx"
        },
        {
          "title": "kleborate",
          "description": "Genotyping and screening of *Klebsiella* genome assemblies.",
          "url": "https://bactopia.github.io/developers/modules/kleborate",
          "path": "/developers/modules/kleborate",
          "tags": [
            "bacteria",
            "klebsiella",
            "amr",
            "virulence",
            "typing",
            "mlst",
            "serotype",
            "k-locus",
            "o-locus",
            "sample-scope"
          ],
          "source_file": "developers/modules/kleborate.mdx"
        },
        {
          "title": "kleborate",
          "description": "Genotyping tool for Klebsiella pneumoniae and its related species complex.",
          "url": "https://bactopia.github.io/developers/subworkflows/kleborate",
          "path": "/developers/subworkflows/kleborate",
          "tags": [
            "klebsiella",
            "pneumoniae",
            "genotyping",
            "virulence",
            "capsule",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/kleborate.mdx"
        },
        {
          "title": "kraken2",
          "description": "Taxonomic classification and host filtering of sequence reads.",
          "url": "https://bactopia.github.io/developers/modules/kraken2",
          "path": "/developers/modules/kraken2",
          "tags": [
            "metagenomics",
            "taxonomy",
            "classification",
            "contamination",
            "scrubbing",
            "k-mer",
            "lca",
            "sample-scope"
          ],
          "source_file": "developers/modules/kraken2.mdx"
        },
        {
          "title": "kraken2",
          "description": "Classify metagenomic reads using Kraken2.",
          "url": "https://bactopia.github.io/developers/subworkflows/kraken2",
          "path": "/developers/subworkflows/kraken2",
          "tags": [
            "metagenomics",
            "taxonomic-classification",
            "kraken2",
            "k-mer",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/kraken2.mdx"
        },
        {
          "title": "legsta",
          "description": "In silico Sequence Based Typing (SBT) of *Legionella pneumophila*.",
          "url": "https://bactopia.github.io/developers/modules/legsta",
          "path": "/developers/modules/legsta",
          "tags": [
            "bacteria",
            "legionella",
            "pneumophila",
            "typing",
            "sbt",
            "mlst",
            "serogroup",
            "sample-scope"
          ],
          "source_file": "developers/modules/legsta.mdx"
        },
        {
          "title": "legsta",
          "description": "In silico Legionella pneumophila Sequence Based Typing.",
          "url": "https://bactopia.github.io/developers/subworkflows/legsta",
          "path": "/developers/subworkflows/legsta",
          "tags": [
            "legionella",
            "pneumophila",
            "sequence-typing",
            "st",
            "epidemiology",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/legsta.mdx"
        },
        {
          "title": "lissero",
          "description": "Predict *Listeria monocytogenes* serogroup.",
          "url": "https://bactopia.github.io/developers/modules/lissero",
          "path": "/developers/modules/lissero",
          "tags": [
            "bacteria",
            "listeria",
            "monocytogenes",
            "serotype",
            "serogroup",
            "typing",
            "pcr",
            "sample-scope"
          ],
          "source_file": "developers/modules/lissero.mdx"
        },
        {
          "title": "lissero",
          "description": "In silico serotype prediction for Listeria monocytogenes.",
          "url": "https://bactopia.github.io/developers/subworkflows/lissero",
          "path": "/developers/subworkflows/lissero",
          "tags": [
            "listeria",
            "monocytogenes",
            "serotype",
            "outbreak",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/lissero.mdx"
        },
        {
          "title": "mash_dist",
          "description": "Calculate genomic distances using MinHash sketches.",
          "url": "https://bactopia.github.io/developers/modules/mash_dist",
          "path": "/developers/modules/mash_dist",
          "tags": [
            "mash",
            "distance",
            "minhash",
            "ani",
            "comparison",
            "taxonomy",
            "sample-scope"
          ],
          "source_file": "developers/modules/mash_dist.mdx"
        },
        {
          "title": "mashdist",
          "description": "Calculate Mash distances between sequences and a reference.",
          "url": "https://bactopia.github.io/developers/subworkflows/mashdist",
          "path": "/developers/subworkflows/mashdist",
          "tags": [
            "mash",
            "distance",
            "minhash",
            "comparison",
            "reference",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/mashdist.mdx"
        },
        {
          "title": "mashtree",
          "description": "Rapid alignment-free phylogenomic tree construction.",
          "url": "https://bactopia.github.io/developers/modules/mashtree",
          "path": "/developers/modules/mashtree",
          "tags": [
            "phylogeny",
            "tree",
            "mash",
            "minhash",
            "alignment-free",
            "distance",
            "clustering",
            "neighbor-joining",
            "run-scope"
          ],
          "source_file": "developers/modules/mashtree.mdx"
        },
        {
          "title": "mashtree",
          "description": "Create phylogenetic trees using Mash distances.",
          "url": "https://bactopia.github.io/developers/subworkflows/mashtree",
          "path": "/developers/subworkflows/mashtree",
          "tags": [
            "phylogeny",
            "tree",
            "mash",
            "distance",
            "comparison",
            "run-scope"
          ],
          "source_file": "developers/subworkflows/mashtree.mdx"
        },
        {
          "title": "mcroni",
          "description": "Detect sequence variations in the *mcr-1* colistin resistance gene.",
          "url": "https://bactopia.github.io/developers/modules/mcroni",
          "path": "/developers/modules/mcroni",
          "tags": [
            "bacteria",
            "amr",
            "resistance",
            "colistin",
            "mcr-1",
            "plasmid",
            "variation",
            "sample-scope"
          ],
          "source_file": "developers/modules/mcroni.mdx"
        },
        {
          "title": "mcroni",
          "description": "Scripts for finding and processing promoter variants upstream of mcr-1.",
          "url": "https://bactopia.github.io/developers/subworkflows/mcroni",
          "path": "/developers/subworkflows/mcroni",
          "tags": [
            "mcr-1",
            "colistin",
            "resistance",
            "promoter",
            "variant",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/mcroni.mdx"
        },
        {
          "title": "meningotype",
          "description": "Serotyping and finetyping of *Neisseria meningitidis*.",
          "url": "https://bactopia.github.io/developers/modules/meningotype",
          "path": "/developers/modules/meningotype",
          "tags": [
            "bacteria",
            "neisseria-meningitidis",
            "serotype",
            "serogroup",
            "finetyping",
            "pora",
            "feta",
            "capsule",
            "sample-scope"
          ],
          "source_file": "developers/modules/meningotype.mdx"
        },
        {
          "title": "meningotype",
          "description": "Predict serotypes of Neisseria meningitidis from genome assemblies.",
          "url": "https://bactopia.github.io/developers/subworkflows/meningotype",
          "path": "/developers/subworkflows/meningotype",
          "tags": [
            "neisseria-meningitidis",
            "serotype",
            "finetype",
            "bexsero",
            "meningococcal",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/meningotype.mdx"
        },
        {
          "title": "merlin",
          "description": "MinER assisted species-specific bactopia tool seLectIoN.",
          "url": "https://bactopia.github.io/developers/subworkflows/merlin",
          "path": "/developers/subworkflows/merlin",
          "tags": [
            "species",
            "identification",
            "typing",
            "serotype",
            "virulence",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/merlin.mdx"
        },
        {
          "title": "merlin_dist",
          "description": "Identify species to trigger genus-specific downstream analyses (Merlin).",
          "url": "https://bactopia.github.io/developers/modules/merlin_dist",
          "path": "/developers/modules/merlin_dist",
          "tags": [
            "merlin",
            "mash",
            "routing",
            "logic",
            "genus-specific",
            "automation",
            "sample-scope"
          ],
          "source_file": "developers/modules/merlin_dist.mdx"
        },
        {
          "title": "merlindist",
          "description": "Identify species from assembly and read data using Mash distances.",
          "url": "https://bactopia.github.io/developers/subworkflows/merlindist",
          "path": "/developers/subworkflows/merlindist",
          "tags": [
            "species",
            "identification",
            "mash",
            "distance",
            "classification",
            "taxonomy",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/merlindist.mdx"
        },
        {
          "title": "midas",
          "description": "Species-level profiling from metagenomic data.",
          "url": "https://bactopia.github.io/developers/subworkflows/midas",
          "path": "/developers/subworkflows/midas",
          "tags": [
            "metagenomics",
            "species",
            "profiling",
            "abundance",
            "strain",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/midas.mdx"
        },
        {
          "title": "midas_download",
          "description": "Download the MIDAS reference database.",
          "url": "https://bactopia.github.io/developers/modules/midas_download",
          "path": "/developers/modules/midas_download",
          "tags": [
            "midas",
            "download",
            "database",
            "metagenomics",
            "species",
            "run-scope"
          ],
          "source_file": "developers/modules/midas_download.mdx"
        },
        {
          "title": "midas_species",
          "description": "Estimate bacterial species abundance from metagenomic reads.",
          "url": "https://bactopia.github.io/developers/modules/midas_species",
          "path": "/developers/modules/midas_species",
          "tags": [
            "metagenomics",
            "abundance",
            "species",
            "midas",
            "marker-genes",
            "diversity",
            "sample-scope"
          ],
          "source_file": "developers/modules/midas_species.mdx"
        },
        {
          "title": "mlst",
          "description": "Automatic Multi-Locus Sequence Typing (MLST) of genome assemblies.",
          "url": "https://bactopia.github.io/developers/modules/mlst",
          "path": "/developers/modules/mlst",
          "tags": [
            "bacteria",
            "typing",
            "mlst",
            "sequence-type",
            "pubmlst",
            "alleles",
            "sample-scope"
          ],
          "source_file": "developers/modules/mlst.mdx"
        },
        {
          "title": "mlst",
          "description": "Determine multilocus sequence types (MLST) from bacterial assemblies.",
          "url": "https://bactopia.github.io/developers/subworkflows/mlst",
          "path": "/developers/subworkflows/mlst",
          "tags": [
            "mlst",
            "sequence-typing",
            "pubmlst",
            "bacteria",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/mlst.mdx"
        },
        {
          "title": "mobsuite",
          "description": "Reconstruct and type plasmids from bacterial genome assemblies.",
          "url": "https://bactopia.github.io/developers/subworkflows/mobsuite",
          "path": "/developers/subworkflows/mobsuite",
          "tags": [
            "plasmid",
            "reconstruction",
            "typing",
            "mobilome",
            "bacterial-genome",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/mobsuite.mdx"
        },
        {
          "title": "mobsuite_recon",
          "description": "Reconstruct and type plasmids from a bacterial genome assembly.",
          "url": "https://bactopia.github.io/developers/modules/mobsuite_recon",
          "path": "/developers/modules/mobsuite_recon",
          "tags": [
            "bacteria",
            "plasmid",
            "reconstruction",
            "mobtyper",
            "replicon",
            "contigs",
            "assembly",
            "sample-scope"
          ],
          "source_file": "developers/modules/mobsuite_recon.mdx"
        },
        {
          "title": "Modules",
          "description": "All available Bactopia modules",
          "url": "https://bactopia.github.io/developers/modules",
          "path": "/developers/modules",
          "tags": [],
          "source_file": "developers/modules/index.mdx"
        },
        {
          "title": "mykrobe",
          "description": "Predict antibiotic resistance from sequence reads.",
          "url": "https://bactopia.github.io/developers/subworkflows/mykrobe",
          "path": "/developers/subworkflows/mykrobe",
          "tags": [
            "bacteria",
            "reads",
            "antimicrobial-resistance",
            "genotype-prediction",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/mykrobe.mdx"
        },
        {
          "title": "mykrobe_predict",
          "description": "Predict Antimicrobial Resistance (AMR) for supported bacterial species.",
          "url": "https://bactopia.github.io/developers/modules/mykrobe_predict",
          "path": "/developers/modules/mykrobe_predict",
          "tags": [
            "amr",
            "resistance",
            "susceptibility",
            "k-mer",
            "fastq",
            "bam",
            "mykrobe",
            "sample-scope"
          ],
          "source_file": "developers/modules/mykrobe_predict.mdx"
        },
        {
          "title": "ncbigenomedownload",
          "description": "Download assemblies and annotation files from NCBI's Assembly database.",
          "url": "https://bactopia.github.io/developers/modules/ncbigenomedownload",
          "path": "/developers/modules/ncbigenomedownload",
          "tags": [
            "ncbi",
            "download",
            "genome",
            "assembly",
            "fasta",
            "genbank",
            "utility",
            "run-scope"
          ],
          "source_file": "developers/modules/ncbigenomedownload.mdx"
        },
        {
          "title": "ncbigenomedownload",
          "description": "Download bacterial genomes from NCBI's RefSeq database.",
          "url": "https://bactopia.github.io/developers/subworkflows/ncbigenomedownload",
          "path": "/developers/subworkflows/ncbigenomedownload",
          "tags": [
            "download",
            "ncbi",
            "refseq",
            "genome",
            "assembly",
            "database",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/ncbigenomedownload.mdx"
        },
        {
          "title": "nf-bactopia Plugin",
          "description": "Developer reference for the nf-bactopia Nextflow plugin -- utility functions used across Bactopia workflows",
          "url": "https://bactopia.github.io/developers/nf-bactopia",
          "path": "/developers/nf-bactopia",
          "tags": [],
          "source_file": "developers/nf-bactopia/index.mdx"
        },
        {
          "title": "ngmaster",
          "description": "Serotyping and Multi-Antigen Sequence Typing (MAST) of *Neisseria gonorrhoeae*.",
          "url": "https://bactopia.github.io/developers/modules/ngmaster",
          "path": "/developers/modules/ngmaster",
          "tags": [
            "bacteria",
            "neisseria-gonorrhoeae",
            "serotype",
            "typing",
            "mast",
            "porb",
            "tbpb",
            "sample-scope"
          ],
          "source_file": "developers/modules/ngmaster.mdx"
        },
        {
          "title": "ngmaster",
          "description": "Perform multi-antigen sequence typing of Neisseria gonorrhoeae from genome assemblies.",
          "url": "https://bactopia.github.io/developers/subworkflows/ngmaster",
          "path": "/developers/subworkflows/ngmaster",
          "tags": [
            "neisseria-gonorrhoeae",
            "ng-mast",
            "typing",
            "gonococcal",
            "antigen",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/ngmaster.mdx"
        },
        {
          "title": "nohuman",
          "description": "Remove human reads from sequencing data using nohuman.",
          "url": "https://bactopia.github.io/developers/subworkflows/nohuman",
          "path": "/developers/subworkflows/nohuman",
          "tags": [
            "human",
            "contamination",
            "decontamination",
            "scrubbing",
            "reads",
            "nohuman",
            "kraken2",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/nohuman.mdx"
        },
        {
          "title": "nohuman_download",
          "description": "Download the nohuman database for human read removal.",
          "url": "https://bactopia.github.io/developers/modules/nohuman_download",
          "path": "/developers/modules/nohuman_download",
          "tags": [
            "bacteria",
            "database",
            "download",
            "human",
            "decontamination",
            "kraken2",
            "nohuman",
            "run-scope"
          ],
          "source_file": "developers/modules/nohuman_download.mdx"
        },
        {
          "title": "nohuman_run",
          "description": "Remove human reads from sequencing data.",
          "url": "https://bactopia.github.io/developers/modules/nohuman_run",
          "path": "/developers/modules/nohuman_run",
          "tags": [
            "human",
            "contamination",
            "decontamination",
            "scrubbing",
            "reads",
            "kraken2",
            "nohuman",
            "sample-scope"
          ],
          "source_file": "developers/modules/nohuman_run.mdx"
        },
        {
          "title": "panaroo",
          "description": "Build a pangenome from GFF3 annotations using Panaroo.",
          "url": "https://bactopia.github.io/developers/subworkflows/panaroo",
          "path": "/developers/subworkflows/panaroo",
          "tags": [
            "pangenome",
            "pan-genome",
            "comparative-genomics",
            "core-genome",
            "alignment",
            "run-scope"
          ],
          "source_file": "developers/subworkflows/panaroo.mdx"
        },
        {
          "title": "panaroo_run",
          "description": "Fast and scalable bacterial pangenome analysis using a graph-based approach.",
          "url": "https://bactopia.github.io/developers/modules/panaroo_run",
          "path": "/developers/modules/panaroo_run",
          "tags": [
            "pan-genome",
            "orthologs",
            "core-genome",
            "gene-presence-absence",
            "graph-based",
            "annotation",
            "run-scope"
          ],
          "source_file": "developers/modules/panaroo_run.mdx"
        },
        {
          "title": "pangenome",
          "description": "Perform pangenome analysis with optional core-genome phylogeny.",
          "url": "https://bactopia.github.io/developers/subworkflows/pangenome",
          "path": "/developers/subworkflows/pangenome",
          "tags": [
            "alignment",
            "core-genome",
            "pan-genome",
            "phylogeny",
            "comparative-genomics",
            "run-scope"
          ],
          "source_file": "developers/subworkflows/pangenome.mdx"
        },
        {
          "title": "pasty",
          "description": "Predict O-antigen serogroup of Pseudomonas aeruginosa isolates.",
          "url": "https://bactopia.github.io/developers/modules/pasty",
          "path": "/developers/modules/pasty",
          "tags": [
            "bacteria",
            "pseudomonas-aeruginosa",
            "serogroup",
            "o-antigen",
            "typing",
            "blast",
            "sample-scope"
          ],
          "source_file": "developers/modules/pasty.mdx"
        },
        {
          "title": "pasty",
          "description": "Predict serogroups of Pseudomonas aeruginosa from assemblies.",
          "url": "https://bactopia.github.io/developers/subworkflows/pasty",
          "path": "/developers/subworkflows/pasty",
          "tags": [
            "pseudomonas-aeruginosa",
            "serogroup",
            "typing",
            "o-antigen",
            "prediction",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/pasty.mdx"
        },
        {
          "title": "pbptyper",
          "description": "Predict Penicillin Binding Protein (PBP) type of *Streptococcus pneumoniae* assemblies.",
          "url": "https://bactopia.github.io/developers/modules/pbptyper",
          "path": "/developers/modules/pbptyper",
          "tags": [
            "bacteria",
            "streptococcus-pneumoniae",
            "penicillin",
            "amr",
            "resistance",
            "pbp",
            "typing",
            "sample-scope"
          ],
          "source_file": "developers/modules/pbptyper.mdx"
        },
        {
          "title": "pbptyper",
          "description": "Predict penicillin binding protein (PBP) types of Streptococcus pneumoniae from genome assemblies.",
          "url": "https://bactopia.github.io/developers/subworkflows/pbptyper",
          "path": "/developers/subworkflows/pbptyper",
          "tags": [
            "streptococcus-pneumoniae",
            "pbp-typing",
            "penicillin",
            "antimicrobial-resistance",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/pbptyper.mdx"
        },
        {
          "title": "phispy",
          "description": "Predict prophage regions integrated into bacterial genomes.",
          "url": "https://bactopia.github.io/developers/modules/phispy",
          "path": "/developers/modules/phispy",
          "tags": [
            "genomics",
            "virus",
            "phage",
            "prophage",
            "bacteriophage",
            "identification",
            "annotation",
            "sample-scope"
          ],
          "source_file": "developers/modules/phispy.mdx"
        },
        {
          "title": "phispy",
          "description": "Prediction of prophages from bacterial genomes.",
          "url": "https://bactopia.github.io/developers/subworkflows/phispy",
          "path": "/developers/subworkflows/phispy",
          "tags": [
            "prophage",
            "phage",
            "bacterial",
            "genome",
            "mobile-genetic-elements",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/phispy.mdx"
        },
        {
          "title": "pirate",
          "description": "Pangenome Identification and Reconciliation Analysis Tool for Epidemiology (PIRATE).",
          "url": "https://bactopia.github.io/developers/modules/pirate",
          "path": "/developers/modules/pirate",
          "tags": [
            "pan-genome",
            "orthologs",
            "core-genome",
            "gene-presence-absence",
            "epidemiology",
            "annotation",
            "run-scope"
          ],
          "source_file": "developers/modules/pirate.mdx"
        },
        {
          "title": "pirate",
          "description": "Build a pangenome from GFF3 annotations using PIRATE.",
          "url": "https://bactopia.github.io/developers/subworkflows/pirate",
          "path": "/developers/subworkflows/pirate",
          "tags": [
            "pangenome",
            "pan-genome",
            "comparative-genomics",
            "core-genome",
            "alignment",
            "run-scope"
          ],
          "source_file": "developers/subworkflows/pirate.mdx"
        },
        {
          "title": "plasmidfinder",
          "description": "Identify plasmid replicon types in bacterial sequences and assemblies.",
          "url": "https://bactopia.github.io/developers/modules/plasmidfinder",
          "path": "/developers/modules/plasmidfinder",
          "tags": [
            "plasmid",
            "replicon",
            "typing",
            "identification",
            "mobility",
            "amr",
            "sample-scope"
          ],
          "source_file": "developers/modules/plasmidfinder.mdx"
        },
        {
          "title": "plasmidfinder",
          "description": "Identify plasmid replicons in bacterial genome assemblies.",
          "url": "https://bactopia.github.io/developers/subworkflows/plasmidfinder",
          "path": "/developers/subworkflows/plasmidfinder",
          "tags": [
            "plasmid",
            "replicon",
            "typing",
            "antimicrobial-resistance",
            "mobilome",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/plasmidfinder.mdx"
        },
        {
          "title": "pneumocat",
          "description": "Capsular typing of Streptococcus pneumoniae from Illumina reads.",
          "url": "https://bactopia.github.io/developers/modules/pneumocat",
          "path": "/developers/modules/pneumocat",
          "tags": [
            "pneumocat",
            "streptococcus-pneumoniae",
            "capsular-typing",
            "serotyping",
            "sample-scope"
          ],
          "source_file": "developers/modules/pneumocat.mdx"
        },
        {
          "title": "pneumocat",
          "description": "Perform capsular typing of Streptococcus pneumoniae from NGS data.",
          "url": "https://bactopia.github.io/developers/subworkflows/pneumocat",
          "path": "/developers/subworkflows/pneumocat",
          "tags": [
            "streptococcus-pneumoniae",
            "serotype",
            "capsular-typing",
            "typing",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/pneumocat.mdx"
        },
        {
          "title": "prokka",
          "description": "Annotate prokaryotic genomes.",
          "url": "https://bactopia.github.io/developers/modules/prokka",
          "path": "/developers/modules/prokka",
          "tags": [
            "prokka",
            "annotation",
            "prokaryotic",
            "bacteria",
            "genbank",
            "gff",
            "sample-scope"
          ],
          "source_file": "developers/modules/prokka.mdx"
        },
        {
          "title": "prokka",
          "description": "Annotate bacterial genomes with functional information.",
          "url": "https://bactopia.github.io/developers/subworkflows/prokka",
          "path": "/developers/subworkflows/prokka",
          "tags": [
            "bacteria",
            "annotation",
            "genome",
            "prokaryote",
            "functional-annotation",
            "genes",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/prokka.mdx"
        },
        {
          "title": "quast",
          "description": "Quality Assessment Tool for Genome Assemblies.",
          "url": "https://bactopia.github.io/developers/modules/quast",
          "path": "/developers/modules/quast",
          "tags": [
            "quast",
            "assembly",
            "quality-control",
            "n50",
            "metrics",
            "sample-scope"
          ],
          "source_file": "developers/modules/quast.mdx"
        },
        {
          "title": "quast",
          "description": "Evaluate assembly quality using QUAST.",
          "url": "https://bactopia.github.io/developers/subworkflows/quast",
          "path": "/developers/subworkflows/quast",
          "tags": [
            "assembly",
            "quality",
            "assessment",
            "metrics",
            "n50",
            "evaluation",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/quast.mdx"
        },
        {
          "title": "rgi",
          "description": "Predict antimicrobial resistance from protein or nucleotide data.",
          "url": "https://bactopia.github.io/developers/subworkflows/rgi",
          "path": "/developers/subworkflows/rgi",
          "tags": [
            "bacteria",
            "assembly",
            "antimicrobial-resistance",
            "resistome",
            "homology",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/rgi.mdx"
        },
        {
          "title": "rgi_heatmap",
          "description": "Create heatmaps of resistance gene presence/absence.",
          "url": "https://bactopia.github.io/developers/modules/rgi_heatmap",
          "path": "/developers/modules/rgi_heatmap",
          "tags": [
            "resistance",
            "antimicrobial-resistance",
            "card",
            "rgi",
            "heatmap",
            "visualization",
            "run-scope"
          ],
          "source_file": "developers/modules/rgi_heatmap.mdx"
        },
        {
          "title": "rgi_main",
          "description": "Predict antibiotic resistance from assemblies.",
          "url": "https://bactopia.github.io/developers/modules/rgi_main",
          "path": "/developers/modules/rgi_main",
          "tags": [
            "resistance",
            "antimicrobial-resistance",
            "card",
            "rgi",
            "amr",
            "sample-scope"
          ],
          "source_file": "developers/modules/rgi_main.mdx"
        },
        {
          "title": "roary",
          "description": "Rapid large-scale prokaryote pan genome analysis.",
          "url": "https://bactopia.github.io/developers/modules/roary",
          "path": "/developers/modules/roary",
          "tags": [
            "pangenome",
            "orthology",
            "core-genome",
            "alignment",
            "bacteria",
            "run-scope"
          ],
          "source_file": "developers/modules/roary.mdx"
        },
        {
          "title": "roary",
          "description": "Build a pangenome from GFF3 annotations using Roary.",
          "url": "https://bactopia.github.io/developers/subworkflows/roary",
          "path": "/developers/subworkflows/roary",
          "tags": [
            "pangenome",
            "pan-genome",
            "comparative-genomics",
            "core-genome",
            "alignment",
            "run-scope"
          ],
          "source_file": "developers/subworkflows/roary.mdx"
        },
        {
          "title": "sccmec",
          "description": "Identify SCCmec elements in Staphylococcus aureus genomes.",
          "url": "https://bactopia.github.io/developers/modules/sccmec",
          "path": "/developers/modules/sccmec",
          "tags": [
            "sccmec",
            "staphylococcus-aureus",
            "mrsa",
            "antimicrobial-resistance",
            "typing",
            "sample-scope"
          ],
          "source_file": "developers/modules/sccmec.mdx"
        },
        {
          "title": "sccmec",
          "description": "Identify SCCmec elements in Staphylococcus aureus genomes.",
          "url": "https://bactopia.github.io/developers/subworkflows/sccmec",
          "path": "/developers/subworkflows/sccmec",
          "tags": [
            "sccmec",
            "staphylococcus-aureus",
            "mrsa",
            "antimicrobial-resistance",
            "typing",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/sccmec.mdx"
        },
        {
          "title": "scoary",
          "description": "Pan-genome wide association studies.",
          "url": "https://bactopia.github.io/developers/modules/scoary",
          "path": "/developers/modules/scoary",
          "tags": [
            "scoary",
            "pangenome",
            "gwas",
            "association",
            "bacteria",
            "roary",
            "run-scope"
          ],
          "source_file": "developers/modules/scoary.mdx"
        },
        {
          "title": "scoary",
          "description": "Pan-genome wide association studies.",
          "url": "https://bactopia.github.io/developers/subworkflows/scoary",
          "path": "/developers/subworkflows/scoary",
          "tags": [
            "gwas",
            "association",
            "pan-genome",
            "traits",
            "statistical",
            "run-scope"
          ],
          "source_file": "developers/subworkflows/scoary.mdx"
        },
        {
          "title": "scrubber",
          "description": "Remove contaminant sequences from metagenomic data.",
          "url": "https://bactopia.github.io/developers/subworkflows/scrubber",
          "path": "/developers/subworkflows/scrubber",
          "tags": [
            "metagenomics",
            "decontamination",
            "human-removal",
            "read-filtering",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/scrubber.mdx"
        },
        {
          "title": "seqsero2",
          "description": "Salmonella serotype prediction from genome sequencing data.",
          "url": "https://bactopia.github.io/developers/modules/seqsero2",
          "path": "/developers/modules/seqsero2",
          "tags": [
            "salmonella",
            "serotype",
            "prediction",
            "seqsero2",
            "antigen",
            "sample-scope"
          ],
          "source_file": "developers/modules/seqsero2.mdx"
        },
        {
          "title": "seqsero2",
          "description": "Predict Salmonella serotypes from genome assemblies.",
          "url": "https://bactopia.github.io/developers/subworkflows/seqsero2",
          "path": "/developers/subworkflows/seqsero2",
          "tags": [
            "salmonella",
            "serotype",
            "prediction",
            "foodborne",
            "enteric",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/seqsero2.mdx"
        },
        {
          "title": "seroba",
          "description": "k-mer based pipeline to identify the serotype of Streptococcus pneumoniae.",
          "url": "https://bactopia.github.io/developers/subworkflows/seroba",
          "path": "/developers/subworkflows/seroba",
          "tags": [
            "streptococcus",
            "pneumoniae",
            "serotype",
            "k-mer",
            "capsular",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/seroba.mdx"
        },
        {
          "title": "seroba_run",
          "description": "k-mer based Streptococcus pneumoniae serotyping.",
          "url": "https://bactopia.github.io/developers/modules/seroba_run",
          "path": "/developers/modules/seroba_run",
          "tags": [
            "streptococcus-pneumoniae",
            "serotype",
            "k-mer",
            "prediction",
            "seroba",
            "sample-scope"
          ],
          "source_file": "developers/modules/seroba_run.mdx"
        },
        {
          "title": "shigapass",
          "description": "Predict Shigella serotypes and differentiate Shigella/EIEC.",
          "url": "https://bactopia.github.io/developers/modules/shigapass",
          "path": "/developers/modules/shigapass",
          "tags": [
            "shigella",
            "eiec",
            "serotype",
            "virulence",
            "prediction",
            "sample-scope"
          ],
          "source_file": "developers/modules/shigapass.mdx"
        },
        {
          "title": "shigapass",
          "description": "Predict serotypes of Shigella from assemblies.",
          "url": "https://bactopia.github.io/developers/subworkflows/shigapass",
          "path": "/developers/subworkflows/shigapass",
          "tags": [
            "shigella",
            "serotype",
            "typing",
            "prediction",
            "antigen-genes",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/shigapass.mdx"
        },
        {
          "title": "shigatyper",
          "description": "Shigella serotype from Illumina or Oxford Nanopore reads.",
          "url": "https://bactopia.github.io/developers/modules/shigatyper",
          "path": "/developers/modules/shigatyper",
          "tags": [
            "shigella",
            "serotype",
            "typing",
            "illumina",
            "nanopore",
            "reads",
            "sample-scope"
          ],
          "source_file": "developers/modules/shigatyper.mdx"
        },
        {
          "title": "shigatyper",
          "description": "Predict serotypes of Shigella from reads or assemblies.",
          "url": "https://bactopia.github.io/developers/subworkflows/shigatyper",
          "path": "/developers/subworkflows/shigatyper",
          "tags": [
            "shigella",
            "serotype",
            "typing",
            "prediction",
            "antigen-genes",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/shigatyper.mdx"
        },
        {
          "title": "shigeifinder",
          "description": "Shigella and EIEC serotyping from assemblies.",
          "url": "https://bactopia.github.io/developers/modules/shigeifinder",
          "path": "/developers/modules/shigeifinder",
          "tags": [
            "shigella",
            "eiec",
            "serotype",
            "identification",
            "cluster",
            "virulence",
            "sample-scope"
          ],
          "source_file": "developers/modules/shigeifinder.mdx"
        },
        {
          "title": "shigeifinder",
          "description": "Predict serotypes of Shigella and EIEC from assemblies.",
          "url": "https://bactopia.github.io/developers/subworkflows/shigeifinder",
          "path": "/developers/subworkflows/shigeifinder",
          "tags": [
            "shigella",
            "eiec",
            "serotype",
            "typing",
            "cluster-analysis",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/shigeifinder.mdx"
        },
        {
          "title": "sistr",
          "description": "Serovar prediction of Salmonella assemblies.",
          "url": "https://bactopia.github.io/developers/modules/sistr",
          "path": "/developers/modules/sistr",
          "tags": [
            "salmonella",
            "serotype",
            "cgmlst",
            "typing",
            "prediction",
            "sample-scope"
          ],
          "source_file": "developers/modules/sistr.mdx"
        },
        {
          "title": "sistr",
          "description": "Salmonella In Silico Typing Resource command-line tool.",
          "url": "https://bactopia.github.io/developers/subworkflows/sistr",
          "path": "/developers/subworkflows/sistr",
          "tags": [
            "salmonella",
            "serotype",
            "mlst",
            "cgmlst",
            "typing",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/sistr.mdx"
        },
        {
          "title": "snippy_core",
          "description": "Core-SNP alignment from Snippy outputs.",
          "url": "https://bactopia.github.io/developers/modules/snippy_core",
          "path": "/developers/modules/snippy_core",
          "tags": [
            "snippy",
            "core-genome",
            "alignment",
            "phylogeny",
            "snp",
            "bacteria",
            "run-scope"
          ],
          "source_file": "developers/modules/snippy_core.mdx"
        },
        {
          "title": "snippy_core",
          "description": "Generate core-genome SNP alignment from per-sample Snippy outputs.",
          "url": "https://bactopia.github.io/developers/subworkflows/snippy_core",
          "path": "/developers/subworkflows/snippy_core",
          "tags": [
            "variant-calling",
            "core-genome",
            "snp",
            "alignment",
            "phylogenetics",
            "run-scope"
          ],
          "source_file": "developers/subworkflows/snippy_core.mdx"
        },
        {
          "title": "snippy_run",
          "description": "Rapid haploid variant calling and core genome alignment.",
          "url": "https://bactopia.github.io/developers/modules/snippy_run",
          "path": "/developers/modules/snippy_run",
          "tags": [
            "snippy",
            "variant-calling",
            "snp",
            "indel",
            "alignment",
            "bacteria",
            "sample-scope"
          ],
          "source_file": "developers/modules/snippy_run.mdx"
        },
        {
          "title": "snippy_run",
          "description": "Call variants against a reference genome using Snippy.",
          "url": "https://bactopia.github.io/developers/subworkflows/snippy_run",
          "path": "/developers/subworkflows/snippy_run",
          "tags": [
            "variant-calling",
            "snp",
            "reference-mapping",
            "phylogenetics",
            "outbreak",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/snippy_run.mdx"
        },
        {
          "title": "snpdists",
          "description": "Create a SNP distance matrix from a multiple sequence alignment.",
          "url": "https://bactopia.github.io/developers/modules/snpdists",
          "path": "/developers/modules/snpdists",
          "tags": [
            "snp",
            "distance",
            "matrix",
            "alignment",
            "phylogeny",
            "run-scope"
          ],
          "source_file": "developers/modules/snpdists.mdx"
        },
        {
          "title": "snpdists",
          "description": "Calculate pairwise SNP distances from sequence alignments.",
          "url": "https://bactopia.github.io/developers/subworkflows/snpdists",
          "path": "/developers/subworkflows/snpdists",
          "tags": [
            "snp",
            "distance",
            "alignment",
            "phylogeny",
            "core-genome",
            "run-scope"
          ],
          "source_file": "developers/subworkflows/snpdists.mdx"
        },
        {
          "title": "spatyper",
          "description": "Finding spa types in Staphylococcus aureus.",
          "url": "https://bactopia.github.io/developers/modules/spatyper",
          "path": "/developers/modules/spatyper",
          "tags": [
            "staphylococcus-aureus",
            "spa-typing",
            "repeat",
            "mrsa",
            "typing",
            "sample-scope"
          ],
          "source_file": "developers/modules/spatyper.mdx"
        },
        {
          "title": "spatyper",
          "description": "Predict spa types of Staphylococcus aureus from genome assemblies.",
          "url": "https://bactopia.github.io/developers/subworkflows/spatyper",
          "path": "/developers/subworkflows/spatyper",
          "tags": [
            "staphylococcus-aureus",
            "spa-typing",
            "protein-a",
            "mrsa",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/spatyper.mdx"
        },
        {
          "title": "srahumanscrubber",
          "description": "Remove human contamination from sequencing reads for SRA submission.",
          "url": "https://bactopia.github.io/developers/subworkflows/srahumanscrubber",
          "path": "/developers/subworkflows/srahumanscrubber",
          "tags": [
            "contamination",
            "human",
            "scrub",
            "sra",
            "sequencing",
            "fastq",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/srahumanscrubber.mdx"
        },
        {
          "title": "srahumanscrubber_initdb",
          "description": "Initialize human read removal database for SRA Human Scrubber.",
          "url": "https://bactopia.github.io/developers/modules/srahumanscrubber_initdb",
          "path": "/developers/modules/srahumanscrubber_initdb",
          "tags": [
            "human",
            "database",
            "scrubber",
            "ncbi",
            "download",
            "sample-scope"
          ],
          "source_file": "developers/modules/srahumanscrubber_initdb.mdx"
        },
        {
          "title": "srahumanscrubber_scrub",
          "description": "Scrub human reads from FASTQ files.",
          "url": "https://bactopia.github.io/developers/modules/srahumanscrubber_scrub",
          "path": "/developers/modules/srahumanscrubber_scrub",
          "tags": [
            "human",
            "contamination",
            "scrubber",
            "decontamination",
            "ncbi",
            "sra",
            "sample-scope"
          ],
          "source_file": "developers/modules/srahumanscrubber_scrub.mdx"
        },
        {
          "title": "ssuissero",
          "description": "Serotype prediction of Streptococcus suis assemblies.",
          "url": "https://bactopia.github.io/developers/modules/ssuissero",
          "path": "/developers/modules/ssuissero",
          "tags": [
            "streptococcus-suis",
            "serotype",
            "typing",
            "prediction",
            "sample-scope"
          ],
          "source_file": "developers/modules/ssuissero.mdx"
        },
        {
          "title": "ssuissero",
          "description": "Predict serotypes of Streptococcus suis from genome assemblies.",
          "url": "https://bactopia.github.io/developers/subworkflows/ssuissero",
          "path": "/developers/subworkflows/ssuissero",
          "tags": [
            "streptococcus-suis",
            "serotype",
            "typing",
            "prediction",
            "capsular-genes",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/ssuissero.mdx"
        },
        {
          "title": "staphopiasccmec",
          "description": "Primer based SCCmec typing of S. aureus genomes.",
          "url": "https://bactopia.github.io/developers/modules/staphopiasccmec",
          "path": "/developers/modules/staphopiasccmec",
          "tags": [
            "staphylococcus-aureus",
            "sccmec",
            "typing",
            "mrsa",
            "primers",
            "sample-scope"
          ],
          "source_file": "developers/modules/staphopiasccmec.mdx"
        },
        {
          "title": "staphopiasccmec",
          "description": "Identify SCCmec elements in Staphylococcus aureus genomes using Staphopia method.",
          "url": "https://bactopia.github.io/developers/subworkflows/staphopiasccmec",
          "path": "/developers/subworkflows/staphopiasccmec",
          "tags": [
            "sccmec",
            "staphylococcus-aureus",
            "mrsa",
            "antimicrobial-resistance",
            "typing",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/staphopiasccmec.mdx"
        },
        {
          "title": "staphtyper",
          "description": "Determine the agr, spa and SCCmec types for _Staphylococcus aureus_ genomes.",
          "url": "https://bactopia.github.io/developers/subworkflows/staphtyper",
          "path": "/developers/subworkflows/staphtyper",
          "tags": [
            "staphylococcus-aureus",
            "agr-typing",
            "spa-typing",
            "sccmec",
            "strain-characterization",
            "run-scope"
          ],
          "source_file": "developers/subworkflows/staphtyper.mdx"
        },
        {
          "title": "stecfinder",
          "description": "Serotype of Shigatoxin producing E. coli using reads/assemblies.",
          "url": "https://bactopia.github.io/developers/modules/stecfinder",
          "path": "/developers/modules/stecfinder",
          "tags": [
            "stec",
            "e.-coli",
            "virulence",
            "serotype",
            "typing",
            "sample-scope"
          ],
          "source_file": "developers/modules/stecfinder.mdx"
        },
        {
          "title": "stecfinder",
          "description": "Identify and serotype Shiga toxin-producing E. coli (STEC) from assemblies.",
          "url": "https://bactopia.github.io/developers/subworkflows/stecfinder",
          "path": "/developers/subworkflows/stecfinder",
          "tags": [
            "escherichia-coli",
            "stec",
            "serotype",
            "virulence-genes",
            "shiga-toxin",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/stecfinder.mdx"
        },
        {
          "title": "Subworkflows",
          "description": "All available Bactopia subworkflows",
          "url": "https://bactopia.github.io/developers/subworkflows",
          "path": "/developers/subworkflows",
          "tags": [],
          "source_file": "developers/subworkflows/index.mdx"
        },
        {
          "title": "sylph",
          "description": "Profile microbial composition using Sylph.",
          "url": "https://bactopia.github.io/developers/subworkflows/sylph",
          "path": "/developers/subworkflows/sylph",
          "tags": [
            "metagenome",
            "profiling",
            "composition",
            "abundance",
            "kmer",
            "taxonomic",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/sylph.mdx"
        },
        {
          "title": "sylph_profile",
          "description": "Profile metagenome samples against a database using Sylph.",
          "url": "https://bactopia.github.io/developers/modules/sylph_profile",
          "path": "/developers/modules/sylph_profile",
          "tags": [
            "metagenomics",
            "profiling",
            "taxonomy",
            "abundance",
            "ani",
            "sylph",
            "sample-scope"
          ],
          "source_file": "developers/modules/sylph_profile.mdx"
        },
        {
          "title": "tblastn",
          "description": "Search protein query sequences against nucleotide database.",
          "url": "https://bactopia.github.io/developers/subworkflows/tblastn",
          "path": "/developers/subworkflows/tblastn",
          "tags": [
            "blast",
            "protein",
            "nucleotide",
            "alignment",
            "database",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/tblastn.mdx"
        },
        {
          "title": "tblastx",
          "description": "Translate nucleotide query sequences and search nucleotide database.",
          "url": "https://bactopia.github.io/developers/subworkflows/tblastx",
          "path": "/developers/subworkflows/tblastx",
          "tags": [
            "blast",
            "nucleotide",
            "translation",
            "alignment",
            "database",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/tblastx.mdx"
        },
        {
          "title": "tbprofiler",
          "description": "Profiling tool for Mycobacterium tuberculosis to detect resistance and strain type.",
          "url": "https://bactopia.github.io/developers/subworkflows/tbprofiler",
          "path": "/developers/subworkflows/tbprofiler",
          "tags": [
            "mycobacterium",
            "tuberculosis",
            "drug-resistance",
            "lineage",
            "variants",
            "sample-scope"
          ],
          "source_file": "developers/subworkflows/tbprofiler.mdx"
        },
        {
          "title": "tbprofiler_collate",
          "description": "Collate TB-Profiler results from multiple samples.",
          "url": "https://bactopia.github.io/developers/modules/tbprofiler_collate",
          "path": "/developers/modules/tbprofiler_collate",
          "tags": [
            "tuberculosis",
            "mycobacterium",
            "drug-resistance",
            "collate",
            "summary",
            "run-scope"
          ],
          "source_file": "developers/modules/tbprofiler_collate.mdx"
        },
        {
          "title": "tbprofiler_profile",
          "description": "Detect resistance and lineages of Mycobacterium tuberculosis genomes.",
          "url": "https://bactopia.github.io/developers/modules/tbprofiler_profile",
          "path": "/developers/modules/tbprofiler_profile",
          "tags": [
            "tuberculosis",
            "mycobacterium",
            "drug-resistance",
            "amr",
            "typing",
            "variant-calling",
            "sample-scope"
          ],
          "source_file": "developers/modules/tbprofiler_profile.mdx"
        },
        {
          "title": "teton",
          "description": "Perform taxonomic classification and estimate bacterial genome sizes.",
          "url": "https://bactopia.github.io/developers/subworkflows/teton",
          "path": "/developers/subworkflows/teton",
          "tags": [
            "metagenomics",
            "taxonomy",
            "classification",
            "kraken",
            "bracken",
            "genome-size",
            "run-scope"
          ],
          "source_file": "developers/subworkflows/teton.mdx"
        }
      ]
    },
    {
      "key": "impact",
      "title": "Impact & Outreach",
      "route_base": "/impact-and-outreach",
      "description": "Citations, acknowledgements, presentations, and community contributions.",
      "page_count": 5,
      "pages": [
        {
          "title": "Impact & Outreach",
          "description": "Discover how Bactopia is making an impact and giving back to the community.",
          "url": "https://bactopia.github.io/impact-and-outreach",
          "path": "/impact-and-outreach",
          "tags": [],
          "source_file": "impact/index.mdx",
          "sidebar_position": 1
        },
        {
          "title": "Acknowledgements",
          "description": "A comprehensive list of datasets and software packages utilized in Bactopia, complete with links and citations.",
          "url": "https://bactopia.github.io/impact-and-outreach/acknowledgements",
          "path": "/impact-and-outreach/acknowledgements",
          "tags": [],
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    },
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          "description": "",
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          "path": "/blog/bactopia-v4",
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  ]
}