Modules

Bactopia includes 98 modules -- individual processes that perform specific analysis tasks. You can also browse by tag.

Module	Description
abricate_run	Mass screening of contigs for antimicrobial and virulence genes.
abricate_summary	Summarize Abricate screening results.
abritamr_run	Detect antimicrobial resistance and virulence genes.
agrvate	Determine the agr locus type and operon variants in Staphylococcus aureus.
amrfinderplus_run	Identify antimicrobial resistance and virulence genes in gene or protein sequences.
amrfinderplus_update	Download and index the latest AMRFinder+ database.
ariba_getref	Download and prepare reference databases for ARIBA analysis.
ariba_run	Identify genes by local assembly of reads.
bactopia_assembler	Assemble bacterial genomes using short read, long read, or hybrid strategies.
bactopia_datasets	Download pre-compiled datasets required by Bactopia.
bactopia_gather	Search, validate, gather, or simulate input samples.
bactopia_qc	Automated quality control, error correction, and read subsampling.
bactopia_sketcher	Create genomic sketches and perform rapid taxonomic classification.
bactopia_teton	Predict genome size and route samples based on taxonomic classification.
bakta_download	Download the Bakta annotation database.
bakta_run	Rapid and standardized annotation of bacterial genomes and plasmids.
blast_blastn	Search a nucleotide database using a nucleotide query.
blast_blastp	Search a protein database using a protein query.
blast_blastx	Search a protein database using a translated nucleotide query.
blast_tblastn	Search a translated nucleotide database using a protein query.
blast_tblastx	Search a translated nucleotide database using a translated nucleotide query.
bracken	Taxonomic classification and abundance estimation.
btyper3	In silico typing and characterization of Bacillus cereus group genomes.
busco	Assess genome assembly completeness using single-copy orthologs.
checkm2_download	Download the pre-trained CheckM2 database.
checkm2_predict	Assess genome quality using machine learning.
checkm_lineagewf	Assess genome quality using lineage-specific marker sets.
clermontyping	Determine the phylogroup of Escherichia coli isolates.
clonalframeml	Inference of recombination in bacterial genomes.
csvtk_concat	Concatenate multiple CSV or TSV files into a single table.
csvtk_join	Join two CSV or TSV files based on common fields.
defensefinder_run	Detect anti-phage defense systems using HMM profiles.
defensefinder_update	Download and package the DefenseFinder and CasFinder model databases.
ectyper	Predict Escherichia coli serotype (O and H antigens).
eggnog_download	Download the eggNOG database for functional annotation.
eggnog_mapper	Functional annotation of proteins using eggNOG orthology data.
emmtyper	emm-typing of Streptococcus pyogenes (Group A Strep) assemblies.
fastani	Compute whole-genome Average Nucleotide Identity (ANI).
gamma	Identification, classification, and annotation of translated gene matches.
genotyphi_parse	Parse Mykrobe results to genotype Salmonella Typhi.
gigatyper	Run all available MLST schemes for a species against an assembly
gtdbtk_classifywf	Taxonomic classification of bacterial and archaeal genomes using GTDB-Tk.
gtdbtk_download	Download and configure the GTDB-Tk reference database.
gubbins	Detect recombination and construct a recombination-free phylogeny.
hicap	Predict Haemophilus influenzae capsule serotype.
hpsuissero	Predict Haemophilus parasuis serotype.
iqtree	Efficient phylogenomic inference using Maximum Likelihood.
ismapper	Identify insertion sites and orientation of mobile genetic elements.
kleborate	Genotyping and screening of Klebsiella genome assemblies.
kraken2	Taxonomic classification and host filtering of sequence reads.
legsta	In silico Sequence Based Typing (SBT) of Legionella pneumophila.
lissero	Predict Listeria monocytogenes serogroup.
mash_dist	Calculate genomic distances using MinHash sketches.
mashtree	Rapid alignment-free phylogenomic tree construction.
mcroni	Detect sequence variations in the mcr-1 colistin resistance gene.
meningotype	Serotyping and finetyping of Neisseria meningitidis.
merlin_dist	Identify species to trigger genus-specific downstream analyses (Merlin).
midas_download	Download the MIDAS reference database.
midas_species	Estimate bacterial species abundance from metagenomic reads.
mlst	Automatic Multi-Locus Sequence Typing (MLST) of genome assemblies.
mobsuite_recon	Reconstruct and type plasmids from a bacterial genome assembly.
mykrobe_predict	Predict Antimicrobial Resistance (AMR) for supported bacterial species.
ncbigenomedownload	Download assemblies and annotation files from NCBI's Assembly database.
ngmaster	Serotyping and Multi-Antigen Sequence Typing (MAST) of Neisseria gonorrhoeae.
nohuman_download	Download the nohuman database for human read removal.
nohuman_run	Remove human reads from sequencing data.
panaroo_run	Fast and scalable bacterial pangenome analysis using a graph-based approach.
pasty	Predict O-antigen serogroup of Pseudomonas aeruginosa isolates.
pbptyper	Predict Penicillin Binding Protein (PBP) type of Streptococcus pneumoniae assemblies.
phispy	Predict prophage regions integrated into bacterial genomes.
pirate	Pangenome Identification and Reconciliation Analysis Tool for Epidemiology (PIRATE).
plasmidfinder	Identify plasmid replicon types in bacterial sequences and assemblies.
pneumocat	Capsular typing of Streptococcus pneumoniae from Illumina reads.
prokka	Annotate prokaryotic genomes.
quast	Quality Assessment Tool for Genome Assemblies.
rgi_heatmap	Create heatmaps of resistance gene presence/absence.
rgi_main	Predict antibiotic resistance from assemblies.
roary	Rapid large-scale prokaryote pan genome analysis.
sccmec	Identify SCCmec elements in Staphylococcus aureus genomes.
scoary	Pan-genome wide association studies.
seqsero2	Salmonella serotype prediction from genome sequencing data.
seroba_run	k-mer based Streptococcus pneumoniae serotyping.
shigapass	Predict Shigella serotypes and differentiate Shigella/EIEC.
shigatyper	Shigella serotype from Illumina or Oxford Nanopore reads.
shigeifinder	Shigella and EIEC serotyping from assemblies.
sistr	Serovar prediction of Salmonella assemblies.
snippy_core	Core-SNP alignment from Snippy outputs.
snippy_run	Rapid haploid variant calling and core genome alignment.
snpdists	Create a SNP distance matrix from a multiple sequence alignment.
spatyper	Finding spa types in Staphylococcus aureus.
srahumanscrubber_initdb	Initialize human read removal database for SRA Human Scrubber.
srahumanscrubber_scrub	Scrub human reads from FASTQ files.
ssuissero	Serotype prediction of Streptococcus suis assemblies.
staphopiasccmec	Primer based SCCmec typing of S. aureus genomes.
stecfinder	Serotype of Shigatoxin producing E. coli using reads/assemblies.
sylph_profile	Profile metagenome samples against a database using Sylph.
tbprofiler_collate	Collate TB-Profiler results from multiple samples.
tbprofiler_profile	Detect resistance and lineages of Mycobacterium tuberculosis genomes.