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File Date Author Commit
 conf 2023-03-03 Keith Jolley Keith Jolley [08533f] Script to run Kleborate and populate database w...
 css 2023-03-23 Keith Jolley Keith Jolley [c93479] Fix HTML closures and tweak CSS.
 datasets 2022-05-24 Keith Jolley Keith Jolley [15103e] Script to autopopulate the town lookup table.
 headers 2020-09-21 Keith Jolley Keith Jolley [1affe6] Use BIGSdb as label in curate_header.html
 images 2023-02-28 Keith Jolley Keith Jolley [c31391] Add screenshot.
 javascript 2023-03-10 Keith Jolley Keith Jolley [769481] Remove logging.
 lib 2023-03-28 Keith Jolley Keith Jolley [bb9d54] Move db changes from v1.43 to 1.42 as this has ...
 scripts 2023-03-28 Keith Jolley Keith Jolley [bb9d54] Move db changes from v1.43 to 1.42 as this has ...
 sql 2023-03-29 Keith Jolley Keith Jolley [d9cc98] Fix change to postgreSQL language definition sy...
 webfonts 2021-07-19 Keith Jolley Keith Jolley [3bf58d] Selector for watermark icon.
 xml 2022-05-23 Keith Jolley Keith Jolley [df45df] Include standard country and year fields in def...
 .perlcriticrc 2017-01-21 Keith Jolley Keith Jolley [800df1] Tweak Perl::Critic directives.
 CITATION 2015-10-20 Keith Jolley Keith Jolley [2961c7] Add CITATION file.
 INSTALL 2016-04-28 Keith Jolley Keith Jolley [840955] Update ReadTheDocs URL.
 LICENSE 2012-08-06 Keith Jolley Keith Jolley [8185ec] Use slimbox2 jQuery plugin for display of charts.
 NOTICE 2017-04-06 Keith Jolley Keith Jolley [588128] Fluid layout of index page using packery.
 README.md 2023-01-18 Keith Jolley Keith Jolley [e2ccca] Version 1.39.1.
 README.txt 2023-02-10 Keith Jolley Keith Jolley [b751e1] Version 1.41.1.
 Upgrading_README.txt 2023-02-01 Keith Jolley Keith Jolley [b0ba6e] Version 1.41.0.
 bigscurate.pl 2018-07-31 Keith Jolley Keith Jolley [a2ca9c] More portable Perl shebang
 bigsdb.pl 2019-02-02 Keith Jolley Keith Jolley [594a7f] Records autotagger and autodefiner jobs in the ...
 bigsjobs.pl 2018-10-18 Keith Jolley Keith Jolley [86280e] Added comment.
 bigsrest.pl 2018-10-22 bryan brancotte bryan brancotte [c69a9b] Use variables from configuration files instead ...

Read Me

Bacterial Isolate Genome Sequence Database (BIGSdb)

Gene-by-gene population annotation and analysis

Written by Keith Jolley, © 2010-2023 University of Oxford

Jolley & Maiden 2010, BMC Bioinformatics 11:595

BIGSdb is software designed to store and analyse sequence data for bacterial
isolates. Any number of sequences can be linked to isolate records - these
can be small contigs assembled from dideoxy sequencing through to whole genomes
(complete or multiple contigs generated from parallel sequencing technologies
such as Illumina).

BIGSdb extends the principle of MLST to genomic data, where large numbers of
loci can be defined, with alleles assigned by reference to sequence definition
databases (which can also be set up with BIGSdb). Loci can also be grouped into
schemes so that types can be defined by combinations of allelic profiles, a
concept analagous to MLST.

The latest version of the BIGSdb documentation can be found at
https://bigsdb.readthedocs.io.