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Microb Genom. 2018 Mar;4(3). doi: 10.1099/mgen.0.000166. Epub 2018 Mar 15.

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

Author information

1
1​Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
2
2​Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
3
3​School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.
4
4​Public Health Services, Ministry of Health, Jerusalem, Israel.

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.

KEYWORDS:

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

PMID:
29543149
PMCID:
PMC5885018
DOI:
10.1099/mgen.0.000166
[Indexed for MEDLINE]
Free PMC Article

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