Bactopia Tools

Bactopia Tools are additional analysis workflows that run specific tools on existing Bactopia results. There are 67 Bactopia Tools available. You can also browse by tag.

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.
agrvate	Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.
amrfinderplus	Bactopia Tool: Amrfinderplus.
ariba	Gene identification through local assemblies.
bakta	Rapid annotation of bacterial genomes and plasmids.
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.
bracken	Estimate taxonomic abundance of metagenomic samples.
btyper3	Taxonomic classification of Bacillus cereus group isolates.
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.
clermontyping	In silico phylotyping of Escherichia genus.
defensefinder	Systematic identification of anti-phage defense systems.
ectyper	In silico prediction of Escherichia coli serotype.
eggnog	Functional annotation of proteins using orthologous groups and phylogenies.
emmtyper	emm-typing of Streptococcus pyogenes assemblies.
fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity.
gamma	Identification, classification, and annotation of translated gene matches.
genotyphi	Salmonella Typhi genotyping with lineage assignment.
gigatyper	Run all available MLST schemes for a species against an assembly
gtdb	Identify marker genes and assign taxonomic classifications using GTDB.
hicap	Identify cap locus serotype and structure in Haemophilus influenzae assemblies.
hpsuissero	Serotype prediction of Haemophilus parasuis assemblies.
ismapper	Identify insertion sequence positions in bacterial genomes.
kleborate	Comprehensive screening of Klebsiella genomes for virulence and resistance determinants.
kraken2	Taxonomic classification of metagenomic sequence reads.
legsta	Sequence Based Typing (SBT) of Legionella pneumophila.
lissero	Serogroup typing prediction for Listeria monocytogenes.
mashdist	Calculate Mash distances between sequences and reference genomes.
mashtree	Rapid phylogenetic tree construction using Mash distances.
mcroni	Sequence variation analysis of mcr-1 genes (mobilized colistin resistance).
meningotype	Comprehensive typing of Neisseria meningitidis.
merlin	MinMER-assisted species-specific tool selection and execution.
midas	Estimate species abundances from metagenomic samples.
mlst	Automatic Multi-Locus Sequence Type (MLST) calling from assembled contigs.
mobsuite	Reconstruction and annotation of plasmids from bacterial genome assemblies.
mykrobe	Antimicrobial resistance detection for specific bacterial species.
ngmaster	Multi-antigen sequence typing of Neisseria gonorrhoeae.
pangenome	Pangenome analysis with optional core-genome phylogeny.
pasty	In silico serogrouping of Pseudomonas aeruginosa isolates.
pbptyper	Penicillin Binding Protein (PBP) typing for Streptococcus pneumoniae.
phispy	Prediction of prophages in bacterial and archaeal genomes.
plasmidfinder	Bactopia Tool: Plasmidfinder.
pneumocat	Capsular type assignment to Streptococcus pneumoniae from sequence reads.
prokka	Rapid whole genome annotation of bacterial, archaeal, and viral genomes.
quast	Quality assessment of assembled contigs using QUAST.
rgi	Prediction of antibiotic resistance genes using RGI.
sccmec	Typing of SCCmec cassettes in Staphylococcus aureus assemblies.
scrubber	Removal of human and contaminant sequences from metagenomic reads.
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.
snippy	Rapid haplotype variant calling and core genome alignment.
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.
sylph	Taxonomic profiling by abundance-corrected MinHash.
tblastn	Search against translated nucleotide databases using protein queries.
tblastx	Search against translated nucleotide databases using translated nucleotide queries.
tbprofiler	Detection of antimicrobial resistance and lineage typing of Mycobacterium tuberculosis.