Bacterial Isolate Genome Sequence Database (BIGSdb)¶
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
- Database setup
- Administrator’s guide
- Types of user
- 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
- Curator’s guide
- Adding new sender details
- Adding new allele sequence definitions
- Updating and deleting allele sequence definitions
- 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
- Uploading sequence contigs linked to isolate records
- Automated web-based sequence tagging
- Projects
- Isolate record versioning
- 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
- Querying isolate data
- Querying by allelic profile
- Retrieving list of isolates or profiles
- 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
- Frequently asked questions (FAQs)
- Appendix