Nice, you're ready to start playing around with Bactopia Tools!. Please if you haven't already, you will need to have completed Using Bactopia.
Bactopia Tools, are additional workflows to further analyze your samples. Using the standard directory structure from Bactopia, Bactopia Tools will automatically import the input files required by a specific tool.
Currently there are over 50, of these Bactopia Tools available!
This section is going to be a little different, you are going to kind of be on your own to explore, so have fun!
- Learn about available Bactopia Tools
- Run multiple Bactopia Tools
First, if you would like, you can head over to Bactopia Tools on the documentation site. Here you can learn alot about the available Bactopia Tools, including:
- Example Usage
- Output Overview
- Parameters
- Citations
But you can also, get a list on the command-line:
bactopia --list_wfs
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bactopia v3.0.0
Bactopia is a flexible pipeline for complete analysis of bacterial genomes
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Below are a list of workflows you can call using the --wf parameter.
Bactopia
bactopia (default) Bactopia is a flexible pipeline for complete analysis of bacterial genomes
cleanyerreads Use Bactopia's read QC steps to Clean-Yer-Reads
staphopia Staphopia is a flexible pipeline for complete analysis of Staphylococcus aureus genomes
teton Host removal and taxon classification with estimated abundances
Bactopia Tools
Bactopia Tools can include multiple tools (Subworkflows) or a single tool (Modules).
Subworkflows (9)
ariba Gene identification through local assemblies
bakta Rapid annotation of bacterial genomes & 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
scrubber Scrub human reads from FASTQ files
snippy Rapid variant calling from Illumina sequence reads with optional core-SNP phylogeny
staphtyper Includes AgrVATE, SpaTyper and Staphopia SCCmec for Staphylococcus aureus
Modules (43)
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
bracken Taxonomic classification ans species abundance estimation of sequence reads
busco Assembly completeness based on evolutionarily informed expectations
checkm Assess the assembly quality of your microbial 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 Rapid Haemophilus parasuis Serotyping of assemblies
ismapper Identify insertion sites positions in bacterial genomes
kleborate Screen for MLST, sub-species, and other Klebsiella related genes of interest
kraken2 Taxonomic classification of sequence reads
legsta Typing of Legionella pneumophila assemblies
lissero Serogroup typing prediction for Listeria monocytogenes
mashdist Calculate Mash distances between sequences
mashtree Create a trees using Mash distance
mcroni Sequence variation in mobilized colistin resistance (mcr-1) genes
meningotype Serotyping of Neisseria meningitidis
midas Estimate species abundances from FASTQ files
mlst Scan contig files against PubMLST typing schemes
mobsuite Reconstruct and annotate plasmids in bacterial assemblies
mykrobe Antimicrobial resistance detection for specific species
ngmaster Multi-antigen sequence typing for Neisseria gonorrhoeae
pasty 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 Rapid Streptococcus suis Serotyping of assemblies
staphopiasccmec Primer based SCCmec typing of Staphylococcus aureus genomes
stecfinder Serotyping Shigella toxin producing Escherichia coli genomes
tbprofiler Detect resistance and lineages of Mycobacterium tuberculosis genomes
updater Update database builds for new Bactopia version
Each one of these Bactopia Tools can be executed by simply changing
the workflow with the --wf parameter.
This is the part where you get to try running Bactopia Tools you might be interested in.
We'll do a few together, let's try pasty first. To do this will need to provide a few parameters
--bactopia and --wf.
The --bactopia parameter should point to the path where your Bactopia outputs are. This will be
the folder before bactopia-samples. In this workshop we didn't change --outdir when running
Bactopia, so the default output folder will be bactopia.
Let's give it a try.
bactopia \
--bactopia bactopia/ \
--wf pasty \
-profile singularity \
--help
Notice I added a --help in there. I want you to be aware that every workflow (--wf) has
its own parameters. If you are ever curious, --help and --help_all are available for
every workflow, with --help_all displaying the hidden parameters.
This time for real.
bactopia \
--bactopia bactopia/ \
--wf pasty \
-profile singularity
When it completes, you will now have a pasty folder for each sample in bactopia-samples.
As well as one in bactopia-comparative which is a concatenation of all the results for
each sample.
Again, from here I think it's time go out and explore.
I hope you were able to run multiple Bactopia Tools, and now understand how
useful they can be in your analysis. One thing to keep in mind, each of these
Bactopia Tools is plug-and-play, so if you can easily move them around. For example,
the staphopia workflow, is just the bactopia workflow with the staphtyper
Bactopia Tool added to it. You can imagine how you might want to always create
a quick tree at the end of a run, for this you could simply add the mashtree
Bactopia Tool to a workflow.
Many many possibilities when it comes to customizing workflows now. Please feel free to keep exploring and playing around.
If you have any issues or feedback, please don't hesitate to reach out!