期刊
MICROBIAL GENOMICS
卷 4, 期 3, 页码 -出版社
MICROBIOLOGY SOC
DOI: 10.1099/mgen.0.000166
关键词
chewBBACA; multilocus sequence typing; schema; gene-by-gene; allele calling
资金
- INNUENDO project - European Food Safety Authority (EFSA) [GP/EFSA/AFSCO/2015/01/CT2]
- ONEIDA project - FEEI - 'Fundos Europeus Estruturais e de Investimento' from 'Programa Operacional Regional Lisboa' [LISBOA-01-0145-FEDER-016417]
- FCT - 'Fundacao para a Ciencia e a Tecnologia', BacGenTrack [FCT/Scientific and Technological Research Council of Turkey (Turkiye Bilimsel ve Teknolojik Arasrrma Kurumu, TUBITAK)] [TUBITAK/0004/2014]
- FEDER [LISBOA-01-0145-FEDER-007391]
- Fundacao para a Ciencia e a Tecnologia
- Fundação para a Ciência e a Tecnologia [TUBITAK/0004/2014] Funding Source: FCT
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.
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