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

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 crea...

Celý popis

Uložené v:
Podrobná bibliografia
Vydané v:Microbial genomics Ročník 4; číslo 3
Hlavní autori: Silva, Mickael, Machado, Miguel P., Silva, Diogo N., Rossi, Mirko, Moran-Gilad, Jacob, Santos, Sergio, Ramirez, Mario, Carriço, João André
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: England Microbiology Society 01.03.2018
Predmet:
Methods Paper
allele calling
chewBBACA
schema
multilocus sequence typing
gene-by-gene
ISSN:2057-5858, 2057-5858
On-line prístup:Získať plný text
Tagy: Pridať tag
Žiadne tagy, Buďte prvý, kto otaguje tento záznam!
Popis
Shrnutí: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 .
Bibliografia:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ISSN:2057-5858
2057-5858
DOI:10.1099/mgen.0.000166