btyper3

Tags: bacillus cereus taxonomy typing toxin-genes sample-scope

In silico taxonomic classification of Bacillus cereus group genomes.

This subworkflow performs taxonomic classification of Bacillus cereus group genomes using BTyper3, which provides comprehensive classification including species, lineage, and toxin gene detection. The results from individual samples are aggregated into a combined summary file.

Take

assembly: Channel<Record>

Field	Description
meta	Groovy Record containing sample information
assembly	Assembly files in FASTA format for Bacillus cereus group classification

Emit

Published

The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.

sample_outputs

Output	Description
tsv	Tab-delimited BTyper3 typing and classification results

run_outputs

Output	Description
csv	Aggregated results in CSV format

Module Composition

This subworkflow calls the following modules:

• csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
• btyper3 - In silico typing and characterization of Bacillus cereus group genomes.

Used By

This subworkflow is used by the following 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