Subworkflows

Bactopia includes 87 subworkflows that orchestrate modules into reusable analysis units. You can also browse by tag.

Subworkflow	Description
abricate	Mass screening of contigs for antimicrobial and virulence genes.
abritamr	Identify antimicrobial resistance genes using AMRFinderPlus.
agrvate	Identify Staphylococcus aureus agr locus type and operon variants.
amrfinderplus	Find antimicrobial resistance genes and point mutations.
ariba	Rapidly identify genes by creating local assemblies from paired-end reads.
bactopia_assembler	Assemble bacterial genomes using automated assembler selection.
bactopia_datasets	Download and provide pre-compiled datasets required by Bactopia.
bactopia_gather	Search, validate, gather, and standardize input samples.
bactopia_qc	Perform comprehensive quality control on sequencing reads.
bactopia_sketcher	Create genomic sketches and perform rapid taxonomic classification.
bakta	Rapid bacterial genome annotation.
blastn	Search a nucleotide database using nucleotide query sequences.
blastp	Search protein sequences against protein database.
blastx	Translate nucleotide sequences and search protein database.
bracken	Estimate species abundance from metagenomic reads.
btyper3	In silico taxonomic classification of Bacillus cereus group genomes.
busco	Assess genome assembly completeness using BUSCO.
checkm	Assess metagenome bin completeness using CheckM.
checkm2	Assess metagenome bin completeness using CheckM2.
clermontyping	Predict phylogroups of Escherichia coli from genome assemblies.
clonalframeml	Detect and mask recombination events in bacterial phylogenies.
defensefinder	Systematically search for anti-phage defense systems.
ectyper	In silico prediction of Escherichia coli serotype.
eggnog	Functional annotation through orthology assignment.
emmtyper	Predict emm types of Streptococcus pyogenes from genome assemblies.
fastani	Calculate Average Nucleotide Identity (ANI) between genomes.
gamma	Gene Allele Mutation Microbial Assessment.
genotyphi	Assign genotypes to Salmonella Typhi genomes.
gigatyper	Run all available MLST schemes for a species against an assembly
gtdb	Taxonomic classification with the Genome Taxonomy Database.
gubbins	Detect and filter recombination regions in bacterial alignments.
hicap	In silico serotyping of the Haemophilus influenzae capsule locus.
hpsuissero	Rapid Haemophilus parasuis serotyping.
iqtree	Construct maximum likelihood phylogenetic trees from alignments.
ismapper	Identify transposase insertion sites in bacterial genomes.
kleborate	Genotyping tool for Klebsiella pneumoniae and its related species complex.
kraken2	Classify metagenomic reads using Kraken2.
legsta	In silico Legionella pneumophila Sequence Based Typing.
lissero	In silico serotype prediction for Listeria monocytogenes.
mashdist	Calculate Mash distances between sequences and a reference.
mashtree	Create phylogenetic trees using Mash distances.
mcroni	Scripts for finding and processing promoter variants upstream of mcr-1.
meningotype	Predict serotypes of Neisseria meningitidis from genome assemblies.
merlin	MinER assisted species-specific bactopia tool seLectIoN.
merlindist	Identify species from assembly and read data using Mash distances.
midas	Species-level profiling from metagenomic data.
mlst	Determine multilocus sequence types (MLST) from bacterial assemblies.
mobsuite	Reconstruct and type plasmids from bacterial genome assemblies.
mykrobe	Predict antibiotic resistance from sequence reads.
ncbigenomedownload	Download bacterial genomes from NCBI's RefSeq database.
ngmaster	Perform multi-antigen sequence typing of Neisseria gonorrhoeae from genome assemblies.
nohuman	Remove human reads from sequencing data using nohuman.
panaroo	Build a pangenome from GFF3 annotations using Panaroo.
pangenome	Perform pangenome analysis with optional core-genome phylogeny.
pasty	Predict serogroups of Pseudomonas aeruginosa from assemblies.
pbptyper	Predict penicillin binding protein (PBP) types of Streptococcus pneumoniae from genome assemblies.
phispy	Prediction of prophages from bacterial genomes.
pirate	Build a pangenome from GFF3 annotations using PIRATE.
plasmidfinder	Identify plasmid replicons in bacterial genome assemblies.
pneumocat	Perform capsular typing of Streptococcus pneumoniae from NGS data.
prokka	Annotate bacterial genomes with functional information.
quast	Evaluate assembly quality using QUAST.
rgi	Predict antimicrobial resistance from protein or nucleotide data.
roary	Build a pangenome from GFF3 annotations using Roary.
sccmec	Identify SCCmec elements in Staphylococcus aureus genomes.
scoary	Pan-genome wide association studies.
scrubber	Remove contaminant sequences from metagenomic data.
seqsero2	Predict Salmonella serotypes from genome assemblies.
seroba	k-mer based pipeline to identify the serotype of Streptococcus pneumoniae.
shigapass	Predict serotypes of Shigella from assemblies.
shigatyper	Predict serotypes of Shigella from reads or assemblies.
shigeifinder	Predict serotypes of Shigella and EIEC from assemblies.
sistr	Salmonella In Silico Typing Resource command-line tool.
snippy_core	Generate core-genome SNP alignment from per-sample Snippy outputs.
snippy_run	Call variants against a reference genome using Snippy.
snpdists	Calculate pairwise SNP distances from sequence alignments.
spatyper	Predict spa types of Staphylococcus aureus from genome assemblies.
srahumanscrubber	Remove human contamination from sequencing reads for SRA submission.
ssuissero	Predict serotypes of Streptococcus suis from genome assemblies.
staphopiasccmec	Identify SCCmec elements in Staphylococcus aureus genomes using Staphopia method.
staphtyper	Determine the agr, spa and SCCmec types for Staphylococcus aureus genomes.
stecfinder	Identify and serotype Shiga toxin-producing E. coli (STEC) from assemblies.
sylph	Profile microbial composition using Sylph.
tblastn	Search protein query sequences against nucleotide database.
tblastx	Translate nucleotide query sequences and search nucleotide database.
tbprofiler	Profiling tool for Mycobacterium tuberculosis to detect resistance and strain type.
teton	Perform taxonomic classification and estimate bacterial genome sizes.