Abstract
Gene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent allele calling in bacterial strains of interest. chewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers. The chewBBACA software uses Python 3.4 or higher and can run on a laptop or in high performance clusters making it useful for both small laboratories and large reference centers. ChewBBACA is available at https://github.com/B-UMMI/chewBBACA.
Highlights
Read mapping approaches using single nucleotide polymorphisms (SNP)/single nucleotide variants (SNV) have been widely used for studying bacterial genomes [1]
This schema can be composed of core loci, which are present in all or the great majority (e.g. 95 %) of the analysed strains, or including all loci detected in the strains of interest
We developed chewBBACA to be a complete stand-alone pipeline for GbG analyses, including constructing and validating novel cg/wgMLST schemas and performing coding sequence (CDS) allele calling suitable for large scale studies. chewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers
Summary
Read mapping approaches using single nucleotide polymorphisms (SNP)/single nucleotide variants (SNV) have been widely used for studying bacterial genomes [1]. We developed chewBBACA to be a complete stand-alone pipeline for GbG analyses, including constructing and validating novel cg/wgMLST schemas and performing CDS allele calling suitable for large scale studies. ChewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers.
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