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...
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| Veröffentlicht in: | Microbial genomics Jg. 4; H. 3 |
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| Sprache: | Englisch |
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01.03.2018
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| ISSN: | 2057-5858, 2057-5858 |
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| 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
. |
|---|---|
| AbstractList | 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
. 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. 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.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. |
| Author | Santos, Sergio Machado, Miguel P. Ramirez, Mario Rossi, Mirko Moran-Gilad, Jacob Carriço, João André Silva, Diogo N. Silva, Mickael |
| Author_xml | – sequence: 1 givenname: Mickael surname: Silva fullname: Silva, Mickael organization: 1Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal – sequence: 2 givenname: Miguel P. surname: Machado fullname: Machado, Miguel P. organization: 1Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal – sequence: 3 givenname: Diogo N. surname: Silva fullname: Silva, Diogo N. organization: 1Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal – sequence: 4 givenname: Mirko surname: Rossi fullname: Rossi, Mirko organization: 2Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland – sequence: 5 givenname: Jacob surname: Moran-Gilad fullname: Moran-Gilad, Jacob organization: 3School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel, 4Public Health Services, Ministry of Health, Jerusalem, Israel – sequence: 6 givenname: Sergio surname: Santos fullname: Santos, Sergio organization: 1Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal – sequence: 7 givenname: Mario surname: Ramirez fullname: Ramirez, Mario organization: 1Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal – sequence: 8 givenname: João André surname: Carriço fullname: Carriço, João André organization: 1Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29543149$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1128/JCM.01193-15 10.1186/1471-2105-6-2 10.1093/bioinformatics/btm404 10.1093/nar/gkf436 10.1073/pnas.95.6.3140 10.1186/1471-2105-11-119 10.1128/CMR.00001-16 10.1093/bioinformatics/bts565 10.1038/nmicrobiol.2016.185 10.1128/JCM.00051-15 10.2807/1560-7917.ES.2017.22.23.30547 10.1099/mgen.0.000146 10.1186/1471-2105-11-595 10.1016/S0022-2836(05)80360-2 10.2807/1560-7917.ES.2017.22.23.30544 10.1101/gr.1224503 |
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| Title | chewBBACA: A complete suite for gene-by-gene schema creation and strain identification |
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