Bacterial Isolate Genome Sequence Database (BIGSdb)
BIGSdb Version 1.47.3
- Written by Keith Jolley
- Copyright © University of Oxford, 2010-2024.
- Jolley & Maiden BMC Bioinformatics 2010, 11:595
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.
- Source code can be downloaded from https://github.com/kjolley/BIGSdb.
Documentation
- The home page for this software is https://pubmlst.org/software/bigsdb/.
- Full documentation can be found at https://bigsdb.readthedocs.io/.
Server status
Cookies
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
| Name | Author | Description | Version | Comments |
|---|---|---|---|---|
| BLAST | Keith Jolley (University of Oxford, UK) | BLAST a query sequence against selected isolate data | 1.6.2 | |
| BURST | Keith Jolley (University of Oxford, UK) | Perform BURST cluster analysis on query results query results | 1.2.4 | Limited to queries with between 2 and 1,000 results. |
| Codon Usage | Keith Jolley (University of Oxford, UK) | Determine codon usage for specified loci for an isolate database query | 1.3.0 | |
| Database Fields | Keith Jolley (University of Oxford, UK) | Display description of fields defined for the current database | 1.1.11 | |
| Field Breakdown | Keith Jolley (University of Oxford, UK) | Breakdown of query results by field | 2.8.0 | |
| Gene Presence | Keith Jolley (University of Oxford, UK) | Analyse presence/absence of loci for dataset generated from query results | 2.2.3 | |
| Genome Comparator | Keith Jolley (University of Oxford, UK) | Compare genomes at defined loci or against loci defined in a reference genome | 2.8.5 | |
| GrapeTree | Keith Jolley (University of Oxford, UK) | Visualization of genomic relationships | 1.5.5 | Limited to queries with between 2 and 10,000 results. |
| iTOL | Keith Jolley (University of Oxford, UK) | Phylogenetic trees with data overlays | 1.6.2 | Limited to queries with between 2 and 2,000 results. |
| Polymorphisms | Keith Jolley (University of Oxford, UK) | Tool for analysing polymorphic sites for particular locus in an isolate dataset | 1.2.1 | Limited to queries with fewer than 2,000 results. |
| Publication Breakdown | Keith Jolley (University of Oxford, UK) | Breakdown of query results by publication | 1.1.11 | |
| ReporTree | Keith Jolley (University of Oxford, UK) | Surveillance-oriented tool to strengthen the linkage between pathogen genetic clusers and epidemiological data | 1.2.0 | Limited to queries with between 2 and 10,000 results. |
| rMLST species identity | Keith Jolley (University of Oxford, UK) | Use rMLST to identify species from bacterial genome assemblies | 2.2.2 | |
| Sequence Bin Breakdown | Keith Jolley (University of Oxford, UK) | Breakdown of sequence bin contig properties | 1.8.2 | |
| SNPsites | Keith Jolley (University of Oxford, UK) | Find SNPs in selected loci | 1.0.0 | Limited to queries with between 2 and 2,000 results. |
| Two Field Breakdown | Keith Jolley (University of Oxford, UK) | Breakdown of one field against another | 1.8.1 | |
| Unique Combinations | Keith Jolley (University of Oxford, UK) | Determine frequencies of unique field combinations | 1.5.0 |
Disabled plugins
| Name | Author | Description | Version | Disabled because |
|---|---|---|---|---|
| Contig export | Keith Jolley (University of Oxford, UK) | Analyse and export contigs selected from query results | 1.2.0 | Not specifically enabled for this database. |
| Export | Keith Jolley (University of Oxford, UK) | Export dataset generated from query results | 1.13.0 | Not specifically enabled for this database. |
| FASTA Export | Keith Jolley (University of Oxford, UK) | Export FASTA file of sequences following an allele attribute query | 2.2.1 | Only for seqdef databases. |
| Kleborate | Keith Jolley (University of Oxford, UK) | Wrapper for Kleborate | 1.0.1 | Not specifically enabled for this database. |
| Locus Explorer | Keith Jolley (University of Oxford, UK) | Tool for analysing allele sequences stored for particular locus | 1.4.2 | Only for seqdef databases. |
| Microreact | Keith Jolley (University of Oxford, UK) | Open data visualization and sharing for genomic epidemiology | 1.4.0 | Not specifically enabled for this database. |
| PCR | Keith Jolley (University of Oxford, UK) | In silico PCR tool for designing and testing primers | 1.0.11 | Not specifically enabled for this database. |
| PhyloViz | Emmanuel Quevillon (Institut Pasteur, Paris); Keith Jolley (University of Oxford, UK) | Creates phylogenetic inference and data visualization for sequence-based typing methods | 1.4.1 | Not specifically enabled for this database. |
| Profile Export | Keith Jolley (University of Oxford, UK) | Export file of allelic profile definitions following a scheme query | 1.5.1 | Only for seqdef databases. |
| Reports | Keith Jolley (University of Oxford, UK) | Prepare formatted isolate reports based on template files | 1.0.0 | Not specifically enabled for this database. |
| Sequence Comparison | Keith Jolley (University of Oxford, UK) | Display a comparison between two sequences | 1.1.0 | Only for seqdef databases. |
| Sequence Export | Keith Jolley (University of Oxford, UK) | Export concatenated allele sequences in XMFA and FASTA formats | 1.9.2 | Not specifically enabled for this database. |
| Sequence Similarity | Keith Jolley (University of Oxford, UK) | Find sequences most similar to selected allele | 1.2.0 | Only for seqdef databases. |
| Sequence Table Export | Keith Jolley (University of Oxford, UK) | Export table of sequences and attributes following an allele attribute query | 1.2.1 | Only for seqdef databases. |