Bacterial Isolate Genome Sequence Database (BIGSdb)
BIGSdb Version 1.19.1
- Written by Keith Jolley
- Copyright © University of Oxford, 2010-2018.
- 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/database/bigsdb/.
- Full documentation can be found at http://bigsdb.readthedocs.io/.
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 | 1.4.4 | |
| BURST | Keith Jolley (University of Oxford, UK) | Perform BURST cluster analysis on query results query results | 1.1.6 | 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 | 1.2.6 | |
| Unique Combinations | Keith Jolley (University of Oxford, UK) | Determine frequencies of unique field combinations | 1.2.0 | |
| Contig export | Keith Jolley (University of Oxford, UK) | Analyse and export contigs selected from query results | 1.1.4 | |
| Database Fields | Keith Jolley (University of Oxford, UK) | Display description of fields defined for the current database | 1.0.4 | |
| Export | Keith Jolley (University of Oxford, UK) | Export dataset generated from query results | 1.6.1 | |
| Genome Comparator | Keith Jolley (University of Oxford, UK) | Compare genomes at defined loci or against loci defined in a reference genome | 2.3.6 | |
| GrapeTree | Keith Jolley (University of Oxford, UK) | Visualization of genomic relationships | 1.0.2 | Limited to queries with between 2 and 10,000 results. |
| iTOL | Keith Jolley (University of Oxford, UK) | Phylogenetic trees with data overlays | 1.3.3 | Limited to queries with between 2 and 2,000 results. |
| Microreact | Keith Jolley (University of Oxford, UK) | Open data visualization and sharing for genomic epidemiology | 1.0.4 | Limited to queries with between 2 and 2,000 results. |
| PhyloViz | Emmanuel Quevillon (Institut Pasteur, Paris) | Creates phylogenetic inference and data visualization for sequence based typing methods | 1.1.2 | Limited to queries with between 2 and 10,000 results. |
| Polymorphisms | Keith Jolley (University of Oxford, UK) | Tool for analysing polymorphic sites for particular locus in an isolate dataset | 1.1.8 | Limited to queries with fewer than 2,000 results. |
| Presence/Absence | Keith Jolley (University of Oxford, UK) | Analyse presence/absence status of loci for dataset generated from query results | 1.1.8 | |
| Publication Breakdown | Keith Jolley (University of Oxford, UK) | Breakdown of query results by publication | 1.1.8 | |
| rMLST species identity | Keith Jolley (University of Oxford, UK) | Query genomes against rMLST species identifier | 1.2.0 | |
| Scheme Breakdown | Keith Jolley (University of Oxford, UK) | Breakdown of scheme fields and alleles | 1.1.10 | |
| Sequence Bin Breakdown | Keith Jolley (University of Oxford, UK) | Breakdown of sequence bin contig properties | 1.4.1 | |
| Sequence Export | Keith Jolley (University of Oxford, UK) | Export concatenated allele sequences in XMFA and FASTA formats | 1.5.14 | |
| Tag Status | Keith Jolley (University of Oxford, UK) | Breakdown status of sequence tagging and designation by locus | 1.2.2 | Limited to queries with fewer than 1,000 results. |
| Disabled plugins | ||||
| Name | Author | Description | Version | Disabled because |
| FASTA Export | Keith Jolley (University of Oxford, UK) | Export FASTA file of sequences following an allele attribute query | 1.0.2 | Only for seqdef databases. |
| Field Breakdown | Keith Jolley (University of Oxford, UK) | Breakdown of query results by field | 1.2.4 | Chartdirector not installed. |
| Locus Explorer | Keith Jolley (University of Oxford, UK) | Tool for analysing allele sequences stored for particular locus | 1.3.7 | Only for seqdef databases. |
| Profile Export | Keith Jolley (University of Oxford, UK) | Export file of allelic profile definitions following a scheme query | 1.0.1 | Only for seqdef databases. |
| Rule Query | Keith Jolley (University of Oxford, UK) | Rule-based sequence scanning and reporting | 1.1.2 | Only for seqdef databases. |
| Sequence Table Export | Keith Jolley (University of Oxford, UK) | Export table of sequences and attributes following an allele attribute query | 1.0.3 | Only for seqdef databases. |
| Sequence Comparison | Keith Jolley (University of Oxford, UK) | Display a comparison between two sequences | 1.0.7 | Only for seqdef databases. |
| Sequence Similarity | Keith Jolley (University of Oxford, UK) | Find sequences most similar to selected allele | 1.1.1 | Only for seqdef databases. |
| Two Field Breakdown | Keith Jolley (University of Oxford, UK) | Two field breakdown | 1.4.6 | Chartdirector not installed. |
Software versions
- Perl 5.016003
- PostgreSQL 9.2.24 on x86_64-redhat-linux-gnu, compiled by gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44), 64-bit
- Apache/2.4.6 (Red Hat Enterprise Linux) OpenSSL/1.0.2k-fips mod_fcgid/2.3.9 mod_perl/2.0.11 Perl/v5.16.3