Bactopia Tools
Bactopia Tools are additional analysis workflows that run specific tools on existing Bactopia results. There are 67 Bactopia Tools available across 9 categories. You can also browse by tag.
Antimicrobial Resistance
Detect and characterize antimicrobial resistance genes, point mutations, and mobilized resistance determinants across bacterial genomes.
| Workflow | Description |
|---|---|
| abricate | Mass screening of contigs for antimicrobial resistance and virulence genes. |
| abritamr | A NATA accredited tool for reporting the presence of antimicrobial resistance genes. |
| amrfinderplus | Bactopia Tool: Amrfinderplus. |
| mcroni | Sequence variation analysis of mcr-1 genes (mobilized colistin resistance). |
| mykrobe | Antimicrobial resistance detection for specific bacterial species. |
| rgi | Prediction of antibiotic resistance genes using RGI. |
| tbprofiler | Detection of antimicrobial resistance and lineage typing of Mycobacterium tuberculosis. |
Annotation
Annotate genome features including genes, proteins, functional domains, prophages, and defense systems.
| Workflow | Description |
|---|---|
| bakta | Rapid annotation of bacterial genomes and plasmids. |
| defensefinder | Systematic identification of anti-phage defense systems. |
| eggnog | Functional annotation of proteins using orthologous groups and phylogenies. |
| gamma | Identification, classification, and annotation of translated gene matches. |
| phispy | Prediction of prophages in bacterial and archaeal genomes. |
| prokka | Rapid whole genome annotation of bacterial, archaeal, and viral genomes. |
Assembly Quality
Evaluate genome assembly completeness, contamination, and overall quality metrics.
| Workflow | Description |
|---|---|
| busco | Assessment of genome assembly completeness using evolutionarily informed expectations. |
| checkm | Assessment of microbial genome assembly quality. |
| checkm2 | Machine learning-based assessment of microbial genome assembly quality. |
| quast | Quality assessment of assembled contigs using QUAST. |
BLAST
Search nucleotide and protein sequences against BLAST databases using all five standard BLAST programs.
| Workflow | Description |
|---|---|
| blastn | Search against nucleotide BLAST databases using nucleotide queries. |
| blastp | Search against protein BLAST databases using protein queries. |
| blastx | Search against protein BLAST databases using translated nucleotide queries. |
| tblastn | Search against translated nucleotide databases using protein queries. |
| tblastx | Search against translated nucleotide databases using translated nucleotide queries. |
Comparative Genomics
Compare genomes through distance estimation, average nucleotide identity, variant calling, pangenome analysis, and phylogenetic tree construction.
| Workflow | Description |
|---|---|
| fastani | Fast alignment-free computation of whole-genome Average Nucleotide Identity. |
| mashdist | Calculate Mash distances between sequences and reference genomes. |
| mashtree | Rapid phylogenetic tree construction using Mash distances. |
| pangenome | Pangenome analysis with optional core-genome phylogeny. |
| snippy | Rapid haplotype variant calling and core genome alignment. |
Metagenomics & Taxonomy
Classify reads taxonomically, estimate species abundances in metagenomic samples, and remove contaminant sequences.
| Workflow | Description |
|---|---|
| bracken | Estimate taxonomic abundance of metagenomic samples. |
| gtdb | Identify marker genes and assign taxonomic classifications using GTDB. |
| kraken2 | Taxonomic classification of metagenomic sequence reads. |
| midas | Estimate species abundances from metagenomic samples. |
| scrubber | Removal of human and contaminant sequences from metagenomic reads. |
| sylph | Taxonomic profiling by abundance-corrected MinHash. |
Plasmids & Mobile Elements
Identify, reconstruct, and type plasmids and insertion sequences from bacterial genome assemblies.
| Workflow | Description |
|---|---|
| ismapper | Identify insertion sequence positions in bacterial genomes. |
| mobsuite | Reconstruction and annotation of plasmids from bacterial genome assemblies. |
| plasmidfinder | Bactopia Tool: Plasmidfinder. |
Typing
Perform multi-locus sequence typing (MLST), phylotyping, and other general sequence-based typing methods.
| Workflow | Description |
|---|---|
| ariba | Gene identification through local assemblies. |
| gigatyper | Run all available MLST schemes for a species against an assembly |
| mlst | Automatic Multi-Locus Sequence Type (MLST) calling from assembled contigs. |
Serotyping & Species-Specific Analysis
Predict serotypes, serogroups, and perform species-specific characterization including specialized typing, virulence screening, and lineage assignment. Many of these tools can be automatically selected and run with merlin based on species identification.
| Workflow | Description |
|---|---|
| agrvate | Rapid identification of Staphylococcus aureus agr locus type and agr operon variants. |
| btyper3 | Taxonomic classification of Bacillus cereus group isolates. |
| clermontyping | In silico phylotyping of Escherichia genus. |
| ectyper | In silico prediction of Escherichia coli serotype. |
| emmtyper | emm-typing of Streptococcus pyogenes assemblies. |
| genotyphi | Salmonella Typhi genotyping with lineage assignment. |
| hicap | Identify cap locus serotype and structure in Haemophilus influenzae assemblies. |
| hpsuissero | Serotype prediction of Haemophilus parasuis assemblies. |
| kleborate | Comprehensive screening of Klebsiella genomes for virulence and resistance determinants. |
| legsta | Sequence Based Typing (SBT) of Legionella pneumophila. |
| lissero | Serogroup typing prediction for Listeria monocytogenes. |
| meningotype | Comprehensive typing of Neisseria meningitidis. |
| merlin | MinMER-assisted species-specific tool selection and execution. |
| ngmaster | Multi-antigen sequence typing of Neisseria gonorrhoeae. |
| pasty | In silico serogrouping of Pseudomonas aeruginosa isolates. |
| pbptyper | Penicillin Binding Protein (PBP) typing for Streptococcus pneumoniae. |
| pneumocat | Capsular type assignment to Streptococcus pneumoniae from sequence reads. |
| sccmec | Typing of SCCmec cassettes in Staphylococcus aureus assemblies. |
| seqsero2 | Salmonella serotype prediction from sequencing reads or assemblies. |
| seroba | Serotyping of Streptococcus pneumoniae from Illumina paired-end reads. |
| shigapass | Prediction of Shigella serotypes and differentiation from EIEC. |
| shigatyper | Rapid determination of Shigella serotypes from sequencing reads. |
| shigeifinder | In silico serotype prediction for Shigella and Enteroinvasive E. coli (EIEC). |
| sistr | Serovar prediction of Salmonella enterica from assemblies. |
| spatyper | spa typing of Staphylococcus aureus assemblies. |
| ssuissero | Serotype prediction of Streptococcus suis assemblies. |
| staphtyper | Comprehensive typing of Staphylococcus aureus genomes. |
| stecfinder | Serotype identification of Shiga toxin-producing E. coli. |