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BIGSdb specifications

Information


Unique identifier OMICS_20820
Name BIGSdb
Alternative name Bacterial Isolate Genome Sequence Database
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.17.1
Stability Stable
Requirements
Apache2 web server with mod_perl2, PostgreSQL database, BioPerl, BLAST+, EMBOSS, infoalign, sixpack, stretcher, Ipcress, Xvfb
Maintained Yes

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Versioning


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Documentation


Maintainers


  • person_outline Keith Jolley
  • person_outline Martin C.J. Maiden

Publications for Bacterial Isolate Genome Sequence Database

BIGSdb citations

 (301)
library_books

Profiling microbial strains in urban environments using metagenomic sequencing data

2018
Biol Direct
PMCID: 5944035
PMID: 29743119
DOI: 10.1186/s13062-018-0211-z

[…] tic pathogenic strains, such as ExPEC E. coli, falling in phylogroup B2 []. MetaMLST detected E. coli in 19 New York subway samples and by comparing the recovered STs with the references available in BigsDB [], we were able to assign the strains to the E. coli phylogroups (Fig. ). The majority (53%) of the samples fall in the mainly non-harmful phylogroup A. One sample harboured a novel E. coli ty […]

library_books

Clonal diversity and genetic profiling of antibiotic resistance among multidrug/carbapenem resistant Klebsiella pneumoniae isolates from a tertiary care hospital in Saudi Arabia

2018
BMC Infect Dis
PMCID: 5934806
PMID: 29724185
DOI: 10.1186/s12879-018-3114-9

[…] Multilocus sequence typing (MLST) was conducted according to the method of Diancourt et al. [] and sequence types (STs) were assigned through the Institut Pasteur (Paris, France) database (http://bigsdb.pasteur.fr/klebsiella/klebsiella.html). Individual locus sequences, as well as the concatenated sequences of all seven MLST loci for each isolate, were analyzed for their diversity using DIVEIN […]

library_books

Genome based analysis of Carbapenemase producing Klebsiella pneumoniae isolates from German hospital patients, 2008 2014

2018
PMCID: 5930415
PMID: 29744043
DOI: 10.1186/s13756-018-0352-y

[…] ermination of capsular type for Klebsiella strains was conducted by wzi gene sequencing extracted from contigs derived from de novo assembly [] and using the websites of the Pasteur Institute (http://bigsdb.pasteur.fr/perl/bigsdb/bigsdb.pl?db=pubmlst_klebsiella_seqdef_public&page=downloadAlleles&scheme_id=4&render=1; last access 25/04/2018). Furthermore, all sequenced genomes were screened for the […]

library_books

Heavy Metal Susceptibility of Escherichia coli Isolated from Urine Samples from Sweden, Germany, and Spain

2018
Antimicrob Agents Chemother
PMCID: 5923176
PMID: 29530862
DOI: 10.1128/AAC.00209-18

[…] ware, with sampling of all odd kmer lengths from 21 to 149. The default optimization parameters were used, together with a minimum contig size of 200 bp and the scaffolding option switched off. Using BIGSdb database software (), multilocus sequence typing was performed according to the seven-gene Achtman scheme (). A neighbor-joining tree was constructed for rMLST () allele nucleotide sequences of […]

library_books

Listeria monocytogenes Source Distribution Analysis Indicates Regional Heterogeneity and Ecological Niche Preference among Serotype 4b Clones

2018
MBio
PMCID: 5904418
PMID: 29666282
DOI: 10.1128/mBio.00396-18

[…] For isolates lacking MLGT haplotype designations, WGS analysis was employed to determine ST and CC. Novel STs were assigned following submission of sequence data to the Listeria MLST database (http://bigsdb.pasteur.fr). A clone corresponded to an MLST-based CC or, for singleton clones, to a ST as described previously (). A MST was constructed using Ridom SeqSphere+ (Ridom GmbH, Muenster, Germany) […]

library_books

A genomic overview of the population structure of Salmonella

2018
PLoS Genet
PMCID: 5886390
PMID: 29621240
DOI: 10.1371/journal.pgen.1007261

[…] es () that were found to be present in ≥98%, intact in ≥94%, and of unexceptional diversity in 3,144 representative Salmonella genomes []. Publicly accessible websites based on the software framework BigsDB [] present cgMLST schemes and their alleles for a variety of bacterial species [,], but not Salmonella, Escherichia, or Yersinia. We therefore developed a website, EnteroBase, which scours all […]

Citations

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BIGSdb institution(s)
Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
BIGSdb funding source(s)
Supported by a Wellcome Trust Biomedical Resource Grant (104992) and the European Community grant FP7-278864-2 (PathoNgenTrace).

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