bigsdb
Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
6 of 8 committers (75.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (4.5%) to scientific vocabulary
Keywords
Repository
Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
Basic Info
- Host: GitHub
- Owner: kjolley
- License: other
- Language: Perl
- Default Branch: develop
- Homepage: https://pubmlst.org/software/bigsdb/
- Size: 386 MB
Statistics
- Stars: 72
- Watchers: 9
- Forks: 22
- Open Issues: 88
- Releases: 76
Topics
Metadata Files
README.md
Bacterial Isolate Genome Sequence Database (BIGSdb)
Gene-by-gene population annotation and analysis
Written by Keith Jolley, 2010-2025 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.
Owner
- Name: Keith Jolley
- Login: kjolley
- Kind: user
- Location: Oxford, UK
- Company: University of Oxford
- Website: https://pubmlst.org/
- Twitter: keithajolley
- Repositories: 14
- Profile: https://github.com/kjolley
Bioinformatician working on microbial genomics at the University of Oxford. Developer of PubMLST and BIGSdb
GitHub Events
Total
- Create event: 30
- Release event: 12
- Issues event: 85
- Watch event: 12
- Delete event: 21
- Issue comment event: 14
- Push event: 371
- Pull request event: 2
Last Year
- Create event: 30
- Release event: 12
- Issues event: 85
- Watch event: 12
- Delete event: 21
- Issue comment event: 14
- Push event: 371
- Pull request event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Keith Jolley | k****y@z****k | 6,029 |
| Keith Jolley | k****y@b****k | 366 |
| horkko | h****o@g****m | 16 |
| bryan brancotte | b****e@p****r | 6 |
| keith | k****h@z****k | 3 |
| BIGSDB User account | b****b@k****r | 1 |
| Benjamin Leopold | b****d@u****e | 1 |
| Jafar Akhondali | j****i@y****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 108
- Total pull requests: 3
- Average time to close issues: 3 months
- Average time to close pull requests: about 14 hours
- Total issue authors: 5
- Total pull request authors: 3
- Average comments per issue: 0.28
- Average comments per pull request: 0.67
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 48
- Pull requests: 1
- Average time to close issues: 9 days
- Average time to close pull requests: about 16 hours
- Issue authors: 3
- Pull request authors: 1
- Average comments per issue: 0.21
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- kjolley (109)
- abrozzi (3)
- bryan-brancotte (2)
- zmeel (1)
- erik-azn (1)
Pull Request Authors
- mikelchtermans (1)
- kjolley (1)
- braffes (1)