chewBBACA: A complete suite for gene-by-gene schema creation and strain identification

Mickael Silva, Miguel P. Machado, Diogo N. Silva, Mirko Rossi, Jacob Moran-Gilad, Sergio Santos, Mario Ramirez, João André Carriço

Research output: Contribution to journalArticlepeer-review

106 Scopus citations

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.

Original languageEnglish
JournalMicrobial genomics
Volume4
Issue number3
DOIs
StatePublished - 1 Mar 2018

Keywords

  • allele calling
  • chewBBACA
  • gene-by-gene
  • multilocus sequence typing
  • schema

ASJC Scopus subject areas

  • Epidemiology
  • Microbiology
  • Molecular Biology
  • Genetics

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