Skip to content


After you've run your samples through Bactopia, you are probably going to want to investigate them some more, or conduct some comparative analyses. That's where Bactopia Tools come into play!

Bactopia Tools are a set of predifined workflows such as pan-genome contruction, serotyping, and phylogenies. A main benefit of using Bactopia Tools, is they make use of the predictable output structure of Bactopia to automate analyses. This saves you valuable time by allowing you to make further use of the many output files to extend your analyses.

Available Bactopia Tools

There are currently 47 Bactopia Tools that you can make use of. Below are a list of available Bactopia Tools, grouped as Subworkflows and Modules.

Subworkflows (8)

Subworkflows string together tools to create an complete pipeline.

Subworkflow Description
ariba Gene identification through local assemblies
bakta Rapid annotation of bacterial genomes and plasmids
eggnog Functional annotation of proteins using orthologous groups and phylogenies
gtdb Identify marker genes and assign taxonomic classifications
merlin MinmER assisted species-specific bactopia tool seLectIoN
pangenome Pangenome analysis with optional core-genome phylogeny
snippy Rapid variant calling from Illumina sequence reads with optional core-SNP phylogeny
staphtyper Determine the agr, spa and SCCmec types for Staphylococcus aureus genomes

Modules (39)

Modules are workflows consisting of only one tool.

Module Description
abricate Mass screening of contigs for antimicrobial and virulence genes
agrvate Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.
amrfinderplus Identify antimicrobial resistance in genes or proteins
busco Assembly completeness based on evolutionarily informed expectations
checkm Assess the assembly quality of your samples
ectyper In-silico prediction of Escherichia coli serotype
emmtyper emm-typing of Streptococcus pyogenes assemblies
fastani fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
gamma Identification, classification, and annotation of translated gene matches
genotyphi Salmonella Typhi genotyping with Mykrobe outputs
hicap Identify cap locus serotype and structure in your Haemophilus influenzae assemblies
hpsuissero Serotype prediction of Haemophilus parasuis assemblies
ismapper Identify insertion sites positions in bacterial genomes
kleborate Screening Klebsiella genome assemblies for MLST, sub-species, and other related genes of interest
kraken Taxonomic classifications of sequence reads
legsta Typing of Legionella pneumophila assemblies
lissero Serogroup typing prediction for Listeria monocytogenes
mashdist Calculate Mash distances between sequences
mashtree Quickly create a tree using Mash distances
mcroni Sequence variation in mcr-1 genes (mobilized colistin resistance)
meningotype Serotyping of Neisseria meningitidis
mlst Automatic MLST calling from assembled contigs
mobsuite Reconstruct and annotate plasmids in bacterial assemblies
mykrobe Antimicrobial resistance detection for specific species
ngmaster Multi-antigen sequence typing for Neisseria gonorrhoeae
pasty in silico serogrouping of Pseudomonas aeruginosa isolates
pbptyper Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae
plasmidfinder Plasmid identification from assemblies
prokka Whole genome annotation of small genomes (bacterial, archeal, viral)
rgi Predict antibiotic resistance from assemblies
seqsero2 Salmonella serotype prediction from reads or assemblies
seroba Serotyping of Streptococcus pneumoniae from sequence reads
shigatyper Shigella serotype from Illumina or Oxford Nanopore reads
shigeifinder Shigella and EIEC serotyping from assemblies
sistr Serovar prediction of Salmonella assemblies
spatyper Computational method for finding spa types in Staphylococcus aureus
ssuissero Serotype prediction of Streptococcus suis assemblies
staphopiasccmec Primer based SCCmec typing of Staphylococcus aureus genomes
tbprofiler Detect resistance and lineages of Mycobacterium tuberculosis genomes

Common Inputs

With the exceptions of the summary tool, each Bactopia Tool will use the following input parameters:

    --bactopia STR          Directory containing Bactopia analysis results for all samples.

    --exclude STR           A text file containing sample names to exclude from the
                                analysis. The expected format is a single sample per line.

    --include STR           A text file containing sample names to include in the
                                analysis. The expected format is a single sample per line.


This parameter tells each tool where to find your Bactopia outputs from your project. Using this path, the tool will identify the required inputs and begin analysis. What this means is there is no need for you to wrangle up input files for comparative analyses.


What --exclude allows is for you to give a text file with a list of samples that should probably be excluded from further analyses. While you can produce this list yourself, the summary tool will produce a list of samples that do not pass certain thresholds. These thresholds are based on read lengths, sequence quality, coverage and assembly quality. You can adjust these thresholds to meet your needs.


Similarly, --include allows you to give a text file with a list of samples to be included in the analysis. This allows you to target your anlyses on a specific subset of samples. An example of this may be to use the fastani tool to determine samples with >95% ANI to a reference, then create a pan-genome with the roary tool using only the subset of samples.

nf-core/modules Availabilty

Good news! All Bactopia Tools are also available through nf-core/modules, a repository of ready to use Nextflow DSL2 modules. This means you can leverage nf-core tools to rapidly string together your own workflows.

Many of the above Bactopia Tools were submitted to nf-core/modules as part of Bactopia V2. The nf-core Team is a fun group to work with so expect many more Bactopia Tools to find their way to nf-core/modules!

Thank you modules team!

Suggest A Tool

Do you have an idea or suggestion for an analysis that should be added to the set of Bactopia Tools? If so, please feel free to submit it to Bactopia GitHub Issues!