Package: btyper3
BTyper3In silicotaxonomic classification ofBacillus cereusgroup isolates using assembled genomesOverviewBTyper3 is a command-line tool for taxonomically classifyingBacillus cereusgroup genomes using a standardized nomenclature.The program, as well as the associated databases, can be downloaded fromhttps://github.com/lmc297/BTyper3.Post issues athttps://github.com/lmc297/BTyper3/issues.For more information, check out the BTyper3 wiki athttps://github.com/lmc297/BTyper3/wiki.InstallationFor more information, check out theBTyper3 wikiconda (recommended)To create a conda environment namedbtyper3and install BTyper3 and all of its dependencies:Installconda, if necessaryCreate a new environment namedbtyper3by running the following command from your terminal:conda create -n btyper3Activate yourbtyper3environment by running the following command from your terminal:conda activate btyper3InstallBTyper3by running the following command from your terminal:conda install -c bioconda btyper3You can now runbtyper3! Run the following command from your terminal to view allbtyper3options, orcheck the BTyper3 wikifor details:btyper3 --helpWhen you're done with BTyper3, you can deactivate thebtyper3environment by running the following:conda deactivatepipTo run BTyper3, please download and install the following dependencies, if necessary:Python 3BLASTv2.9.0+ and upAdd BLAST+ to your path, if necessary (to check if BLAST+ is in your path, try runningmakeblastdb -handtblastn -hfrom your command line; you should get a help message for each command, with no error messages)Install viapip(this will download required Python dependencies as well):pip install btyper3News: updates in BTyper3 v3.2.0, v3.3.0, and v3.4.0 -- new species just dropped!The primary function of BTyper3 is to allow users to taxonomically classifyB. cereusgroup genomes using a standardized nomenclature (seehereandherefor details regarding how the standardized nomenclature was constructed, and how it compares to historical typing methods, respectively). However, we understand that some users may also want to compare theirB. cereusgroup genomes to the type strain genomes of publishedB. cereusgroup species. Thus, in BTyper3 v3.2.0, we have added the--ani_typestrainsoption, which calculates ANI values between a query genome and the genomes of all publishedB. cereusgroup species type strains and reports the type strain that produces the highest ANI value.The type strain genomes used by BTyper3's--ani_typestrainsoption correspond to the species discussed inFigure 2 of our taxonomy review, plus species published after the review was published (i.e.,Bacillus sanguinis,Bacillus paramobilis, andBacillus hominis, added in v3.2.0; "B. arachidis" andB. rhizoplanae, added in v3.3.0; "B. pretiosus", added in v3.4.0). Within the standardized taxonomy that BTyper3 uses for genomospecies assignment:All members ofBacillus sanguinis(type strain RefSeq Assembly Accession GCF_018332475.1) belong toB. mosaicus(i.e.,B. sanguinisis not considered a novel species in the standardized taxonomy)All members ofBacillus paramobilis(type strain RefSeq Assembly Accession GCF_018332495.1) belong toB. mosaicus(i.e.,B. paramobilisis not considered a novel species in the standardized taxonomy)All members ofBacillus hominis(type strain RefSeq Assembly Accession GCF_018332515.1) belong toB. mycoides(i.e.,B. hominisis not considered a novel species in the standardized taxonomy)"Bacillus arachidis" (type strain RefSeq Assembly Accession GCF_017498775.1) replaces the putative genomospecies previously referred to as "Unknown Species 17" in the standardized taxonomyBacillus rhizoplanae(type strain RefSeq Assembly Accession GCF_917563915.1) represents a novel genomospecies within the standardized taxonomy and has been added to the databaseAll members of "Bacillus pretiosus" (type strain RefSeq Assembly Accession GCF_025916425.1) belong toB. mosaicus(i.e., "B. pretiosus" is not considered a novel species in the standardized taxonomy)Importantly,B. cereusgroup species are often proposed in the literature using unstandardized approaches(e.g., varying genomospecies thresholds, which may produce overlapping genomospecies). We have added the type strain comparison method in BTyper3 v3.2.0, as users may still want to compare a query genome with the type strains of publishedB. cereusgroup species. However, interpret results with caution, as someB. cereusgroup genomes may belong to multiple species using type strain genomes.For more information, check out our:Review ofB. cereusgroup taxonomy/nomenclatureStandardized nomenclature for theB. cereusgroupComparison of our standardized nomenclature to otherB. cereusgroup typing methods (e.g., MLST,panC, ANI-based comparisons to species type strain genomes)CitationIf you found the BTyper3 tool, its source code, and/or any of its associated databases useful, please cite:Carroll, Laura M., Martin Wiedmann, Jasna Kovac. 2020."Proposal of a Taxonomic Nomenclature for theBacillus cereusGroup Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes."mBio11(1): e00034-20; DOI: 10.1128/mBio.00034-20.Carroll, Laura M., Rachel A. Cheng, Jasna Kovac. 2020."No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for theBacillus cereusgroup with Historical Typing Methods."Frontiers in Microbiology11: 580691; DOI: 10.3389/fmicb.2020.580691.Quick StartFor detailed information, check out theBTyper3 wikiCommand Structurebtyper3 -i [fasta] -o [output directory] [options...]For help, typebtyper3 -horbtyper3 --helpFor your current version, typebtyper3 --versionSample CommandsPerform all default analyses, using an assembled genome (complete or draft) in (multi-)FASTA format as input (assumes fastANI is in the user's path):btyper3 -i /path/to/genome.fasta -o /path/to/desired/output_directoryPerform all default analyses, using an assembled genome (complete or draft) in (multi-)FASTA format as input (fastANI is not in the user's path):btyper3 -i /path/to/genome.fasta -o /path/to/desired/output_directory --fastani_path /path/to/FastANI_executable/fastANIPerform all default analyses, plus pseudo-gene flow unit assignment, using an assembled genome (complete or draft) in (multi-)FASTA format as input (assumes fastANI is in the user's path):btyper3 -i /path/to/genome.fasta -o /path/to/desired/output_directory --ani_geneflow TruePerform seven-gene MLST only, using user-supplied MLST gene sequences and the latest version of the PubMLSTB. cereus s.l.database (sequences can be in multi-FASTA format, or concatenated into a single sequence in FASTA format):btyper3 -i /path/to/mlst.fasta -o /path/to/desired/output_directory --ani_species False --ani_subspecies False --ani_typestrains False --virulence False --bt False --panC False --download_mlst_latest TruePerformpanCgroup assignment only, using a user-suppliedpanCgene sequence in FASTA format:btyper3 -i /path/to/panC.fasta -o /path/to/desired/output_directory --ani_species False --ani_subspecies False --ani_typestrains False --virulence False --bt False --mlst FalsePerform virulence factor and Bt toxin-encoding gene detection in a plasmid sequence in FASTA format:btyper3 -i /path/to/plasmid.fasta -o /path/to/desired/output_directory --ani_species False --ani_subspecies False --ani_typestrains False --mlst False --panC FalseDisclaimer: BTyper3 is pretty neat! However, no tool is perfect, and BTyper3 cannot definitively prove whether an isolate is pathogenic or not. As always, interpret your results with caution. We are not responsible for taxonomic misclassifications, misclassifications of an isolate's pathogenic potential or industrial utility, and/or misinterpretations (biological, statistical, or otherwise) of BTyper3 results.