Bacterial Isolate Genome Sequence Database (BIGSdb)

BIGSdb Version 1.43.1

BIGSdb is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

BIGSdb is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Full details of the GNU General Public License can be found at http://www.gnu.org/licenses/gpl.html.

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Installed plugins

Plugins may be disabled by the system administrator for specific databases where either they're not appropriate or if they may take up too many resources on a public database.

Enabled plugins

NameAuthorDescriptionVersionComments
BLASTKeith Jolley (University of Oxford, UK)BLAST a query sequence against selected isolate data1.5.3
BURSTKeith Jolley (University of Oxford, UK)Perform BURST cluster analysis on query results query results1.2.1Limited to queries with between 2 and 1,000 results.
Codon UsageKeith Jolley (University of Oxford, UK)Determine codon usage for specified loci for an isolate database query1.2.15
Unique CombinationsKeith Jolley (University of Oxford, UK)Determine frequencies of unique field combinations1.4.7
Contig exportKeith Jolley (University of Oxford, UK)Analyse and export contigs selected from query results1.1.13
Database FieldsKeith Jolley (University of Oxford, UK)Display description of fields defined for the current database1.1.8
ExportKeith Jolley (University of Oxford, UK)Export dataset generated from query results1.9.5
Field BreakdownKeith Jolley (University of Oxford, UK)Breakdown of query results by field2.6.1
Gene PresenceKeith Jolley (University of Oxford, UK)Analyse presence/absence of loci for dataset generated from query results2.1.0
Genome ComparatorKeith Jolley (University of Oxford, UK)Compare genomes at defined loci or against loci defined in a reference genome2.7.7
GrapeTreeKeith Jolley (University of Oxford, UK)Visualization of genomic relationships1.5.5Limited to queries with between 2 and 10,000 results.
iTOLKeith Jolley (University of Oxford, UK)Phylogenetic trees with data overlays1.5.8Limited to queries with between 2 and 2,000 results.
MicroreactKeith Jolley (University of Oxford, UK)Open data visualization and sharing for genomic epidemiology1.3.0Limited to queries with between 2 and 2,000 results.
PCRKeith Jolley (University of Oxford, UK)In silico PCR tool for designing and testing primers1.0.10
PhyloVizEmmanuel Quevillon (Institut Pasteur, Paris);
Keith Jolley (University of Oxford, UK)
Creates phylogenetic inference and data visualization for sequence-based typing methods1.3.2Limited to queries with between 2 and 10,000 results.
PolymorphismsKeith Jolley (University of Oxford, UK)Tool for analysing polymorphic sites for particular locus in an isolate dataset1.1.14Limited to queries with fewer than 2,000 results.
Publication BreakdownKeith Jolley (University of Oxford, UK)Breakdown of query results by publication1.1.11
rMLST species identityKeith Jolley (University of Oxford, UK)Use rMLST to identify species from bacterial genome assemblies2.2.1
ReporTreeKeith Jolley (University of Oxford, UK)Surveillance-oriented tool to strengthen the linkage between pathogen genetic clusers and epidemiological data1.1.0Limited to queries with between 2 and 10,000 results.
Sequence Bin BreakdownKeith Jolley (University of Oxford, UK)Breakdown of sequence bin contig properties1.7.3
Sequence ExportKeith Jolley (University of Oxford, UK)Export concatenated allele sequences in XMFA and FASTA formats1.7.6
Two Field BreakdownKeith Jolley (University of Oxford, UK)Breakdown of one field against another1.7.1

Disabled plugins

NameAuthorDescriptionVersionDisabled because
FASTA ExportKeith Jolley (University of Oxford, UK)Export FASTA file of sequences following an allele attribute query2.0.2Only for seqdef databases.
KleborateKeith Jolley (University of Oxford, UK)Wrapper for Kleborate1.0.1Not specifically enabled for this database.
Locus ExplorerKeith Jolley (University of Oxford, UK)Tool for analysing allele sequences stored for particular locus1.3.16Only for seqdef databases.
Profile ExportKeith Jolley (University of Oxford, UK)Export file of allelic profile definitions following a scheme query1.3.2Only for seqdef databases.
ReportsKeith Jolley (University of Oxford, UK)Prepare formatted isolate reports based on template files1.0.0Not specifically enabled for this database.
Sequence Table ExportKeith Jolley (University of Oxford, UK)Export table of sequences and attributes following an allele attribute query1.2.0Only for seqdef databases.
Sequence ComparisonKeith Jolley (University of Oxford, UK)Display a comparison between two sequences1.0.11Only for seqdef databases.
Sequence SimilarityKeith Jolley (University of Oxford, UK)Find sequences most similar to selected allele1.1.4Only for seqdef databases.