btyper3

Tags: bacteria bacillus cereus typing virulence toxin amr mlst sample-scope

In silico typing and characterization of Bacillus cereus group genomes.

Uses BTyper3 to classify B. cereus group isolates. It determines the PanC clade, Multi-Locus Sequence Type (MLST), and screens for virulence factors, crystal toxins (Bt), and antimicrobial resistance genes.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

Outputs

record (
    meta: Record,
    tsv: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Tab-delimited Bacillus cereus group typing results including PanC clade and virulence factors
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

BTyper3 Parameters

Parameter	Type	Default	Description
--btyper3_virulence_identity	integer	70	Minimum percent amino acid/nucleotide identity threshold for a virulence gene to be considered present
--btyper3_identity	integer	50	Minimum percent amino acid identity threshold for a Bt toxin gene to be considered present
--btyper3_opts	string		Additional options to pass to BTyper3

Used By

Subworkflows

• btyper3 - In silico taxonomic classification of Bacillus cereus group genomes.

Workflows

• btyper3 - Taxonomic classification of Bacillus cereus group isolates.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• BTyper3
  Carroll LM, Cheng RA, Kovac J No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods. Frontiers in Microbiology, 11, 580691. (2020)

Source

View source on GitHub

Version

BTYPER3:
    - btyper3: 3.4.0