Bacterial Isolate Genome Sequence Database (BIGSdb)ΒΆ
Gene-by-gene population annotation and analysis
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 454 or 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 software has been released under the GNU General Public Licence version 3. The latest version of this documentation can be found at http://bigsdb.readthedocs.org/.
- Concepts and terms
- BIGSdb dependencies
- Installation and configuration of BIGSdb
- Software installation
- Configuring PostgreSQL
- Site-specific configuration
- Setting up the offline job manager
- Setting up the submission system
- Periodically delete temporary files
- Prevent preference database getting too large
- Purging old jobs from the jobs database
- Log file rotation
- Upgrading BIGSdb
- Running the BIGSdb RESTful interface
- Database setup
- Administrator’s guide
- Types of user
- User groups
- Curator permissions
- Locus and scheme permissions (sequence definition database)
- Controlling access
- Setting user passwords
- Setting the first user password
- Enabling plugins
- Temporarily disabling database updates
- Host mapping
- Improving performance
- Dataset partitioning
- Adding new loci
- Defining locus extended attributes
- Defining schemes
- Organizing schemes into hierarchical groups
- Setting up client databases
- Rule-based sequence queries
- Workflow for setting up a MLST scheme
- Defining new loci based on annotated reference genome
- Genome filtering
- Setting locus genome positions
- Defining composite fields
- Extended provenance attributes (lookup tables)
- Sequence bin attributes
- Checking external database configuration settings
- Exporting table configurations
- Authorizing third-party client software to access authenticated resources
- Curator’s guide
- Adding new sender details
- Adding new allele sequence definitions
- Updating and deleting allele sequence definitions
- Retiring allele identifiers
- Updating locus descriptions
- Adding new scheme profile definitions
- Updating and deleting scheme profile definitions
- Adding isolate records
- Updating and deleting single isolate records
- Batch updating multiple isolate records
- Deleting multiple isolate records
- Linking isolate records to publications
- Uploading sequence contigs linked to isolate records
- Automated web-based sequence tagging
- Projects
- Isolate record versioning
- Curating submitted data
- Offline curation tools
- Definition downloads
- Data records
- Querying data
- Querying sequences to determine allele identity
- Searching for specific allele definitions
- Browsing scheme profile definitions
- Querying scheme profile definitions
- Investigating allele differences
- Browsing isolate data
- Querying isolate data
- Querying by allelic profile
- Retrieving isolates by linked publication
- User-configurable options
- Data analysis plugins
- Locus explorer
- Field breakdown
- Two field breakdown
- Scheme and allele breakdown
- Sequence bin breakdown
- Genome comparator
- BLAST
- BURST
- Codon usage
- Unique combinations
- Polymorphisms
- Presence/absence
- Tag status
- Data export plugins
- Submitting data using the submission system
- RESTful Application Programming Interface (API)
- Passing additional/optional parameters
- Resources
- GET / or /db - List site resources
- GET /db/{database} - List database resources
- GET /db/{database}/loci - List loci
- GET /db/{database}/loci/{locus} - Retrieve locus record
- GET /db/{database}/loci/{locus}/alleles - Retrieve list of alleles defined for a locus
- GET /db/{database}/loci/{locus}/alleles_fasta - Download alleles in FASTA format
- GET /db/{database}/loci/{locus}/alleles/{allele_id} - Retrieve full allele information
- GET /db/{database}/schemes - List schemes
- GET /db/{database}/schemes/{scheme_id} - Retrieve scheme information
- GET /db/{database}/schemes/{scheme_id}/fields/{field} - Retrieve information about scheme field
- GET /db/{database}/schemes/{scheme_id}/profiles - List allelic profiles defined for scheme
- GET /db/{database}/schemes/{scheme_id}/profiles_csv - Download allelic profiles in CSV (tab-delimited) format
- GET /db/{database}/schemes/{scheme_id}/profiles/{profile_id} - Retrieve allelic profile record
- GET /db/{database}/isolates - Retrieve list of isolate records
- GET /db/{database}/isolates/{isolate_id} - Retrieve isolate record
- GET /db/{database}/isolates/{isolate_id}/allele_designations - Retrieve list of allele designation records
- GET /db/{database}/isolates/{isolate_id}/allele_designations/{locus} - Retrieve full allele designation record
- GET /db/{database}/isolates/{isolate_id}/allele_ids - Retrieve allele identifiers
- GET /db/{database}/isolates/{isolate_id}/schemes/{scheme_id}/allele_designations - Retrieve scheme allele designation records
- GET /db/{database}/isolates/{isolate_id}/schemes/{scheme_id}/allele_ids - Retrieve list of scheme allele identifiers
- GET /db/{database}/isolates/{isolate_id}/contigs - Retrieve list of contigs
- GET /db/{database}/isolates/{isolate_id}/contigs_fasta - Download contigs in FASTA format
- GET /db/{database}/contigs/{contig_id} - Retrieve contig record
- GET /db/{database}/fields - Retrieve list of isolate provenance field descriptions
- GET /db/{database}/users/{user_id} - Retrieve user information
- GET /db/{database}/projects - Retrieve list of projects
- GET /db/{database}/projects/{project_id} - Retrieve project information
- GET /db/{database}/projects/{project_id}/isolates - Retrieve list of isolates belonging to a project
- GET /db/{database}/submissions - retrieve list of submissions
- POST /db/{database}/submissions - create new submission
- GET /db/{database}/submissions/{submission_id} - Retrieve submission record
- DELETE /db/{database}/submissions/{submission_id} - Delete submission record
- GET /db/{database}/submissions/{submission_id}/messages - Retrieve submission correspondence
- POST /db/{database}/submissions/{submission_id}/messages - Add submission correspondence
- GET /db/{database}/submissions/{submission_id}/files - Retrieve list of supporting files uploaded for submission
- POST /db/{database}/submissions/{submission_id}/files - Upload submission supporting file
- GET /db/{database}/submissions/{submission_id}/files/{filename} - Download submission supporting file
- DELETE /db/{database}/submissions/{submission_id}/files/{filename} - Delete submission supporting file
- Authentication
- Frequently asked questions (FAQs)
- Appendix
- Database schema