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
  • Loci
  • Alleles
  • Schemes
  • Profiles
  • Classification groups
  • Sequence tags
  • Sets
• BIGSdb dependencies
  • Required packages
    • Linux packages
    • Perl modules
    • Optional packages
• Installation and configuration of BIGSdb
  • Software installation
  • Configuring PostgreSQL
    • pg_hba.conf
    • pg_ident.conf
  • Setting global connection parameters
  • Site-specific configuration
  • Setting up the offline job manager
  • Setting up the submission system
  • Setting up a site-wide user database
  • 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
    • Proxying the API to use a standard web port
• Database setup
  • Creating databases
  • Database-specific configuration
  • XML configuration attributes used in config.xml
    • Isolate database XML attributes
      • Special values
    • Sequence definition database XML attributes
  • Over-riding global defaults set in bigsdb.conf
  • Over-riding values set in config.xml
  • User authentication
    • Apache authentication
    • Built-in authentication
  • Setting up the admin user
  • Updating PubMed citations
  • Configuring access to remote contigs
    • Setting up authentication
    • Processing remote contigs
• Administrator’s guide
  • Types of user
  • User groups
  • Curator permissions
  • Locus and scheme permissions (sequence definition database)
  • Controlling access
    • Restricting particular configurations to specific user accounts
  • Setting user passwords
  • Setting the first user password
  • Enabling plugins
  • Temporarily disabling database updates
    • Global
    • Database-specific
  • Host mapping
  • Improving performance
    • Use mod_perl
    • Cache scheme definitions within an isolate database
    • Use a ramdisk for the secure temporary directory
  • Dataset partitioning
    • Sets
    • Configuration of sets
    • Set metadata
    • Set views
    • Using only defined sets
  • Setting a site-wide users database
  • Adding new loci
    • Sequence definition databases
      • Single locus
      • Batch adding
    • Isolate databases
      • Single locus
      • Batch adding
  • Defining locus extended attributes
  • Defining schemes
    • Sequence definition databases
    • Isolate databases
  • Organizing schemes into hierarchical groups
  • Setting up client databases
    • Look up isolates with given allele
    • Look up isolates with a given scheme primary key
    • Look up specific isolate database fields linked to a given allele
  • Rule-based sequence queries
    • Example rule code
      • Rule files
      • Linking to the rule query
      • Adding descriptive text
  • Workflow for setting up a MLST scheme
  • Automated assignment of scheme profiles
  • Scheme profile clustering - setting up classification schemes
    • Defining classification scheme in sequence definition database
    • Defining classification scheme in isolate database
    • Clustering
  • Defining new loci based on annotated reference genome
  • Genome filtering
    • Filtering by in silico PCR
    • Filtering by in silico hybridization
  • 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
    • Single allele
    • Batch adding multiple alleles
      • Upload using a spreadsheet
      • Upload using a FASTA file
  • Updating and deleting allele sequence definitions
  • Retiring allele identifiers
  • Updating locus descriptions
  • Adding new scheme profile definitions
  • Updating and deleting scheme profile definitions
  • Retiring scheme profile definitions
  • Adding isolate records
  • Updating and deleting single isolate records
  • Batch updating multiple isolate records
  • Deleting multiple isolate records
  • Retiring isolate identifiers
  • Setting alternative names for isolates (aliases)
  • Linking isolate records to publications
  • Uploading sequence contigs linked to an isolate record
    • Select isolate from drop-down list
    • Select from isolate query
    • Upload options
  • Batch uploading sequence contigs linked to multiple isolate records
  • Linking remote contigs to isolate records
  • Automated web-based sequence tagging
  • Projects
    • Creating the project
    • Explicitly adding isolates to a project
  • Isolate record versioning
• Curating submitted data
  • Alleles
    • Individual allele curation
    • Batch allele curation
    • Rejecting sequences
    • Requesting additonal information
    • Closing the submission
  • Profiles
    • Individual profile curation
    • Batch profile curation
    • Rejecting profiles
    • Requesting additonal information
    • Closing the submission
  • Isolates
    • Requesting additonal information
    • Closing the submission
• Offline curation tools
  • Automated offline sequence tagging
  • Defining exemplar alleles
  • Automated offline allele definition
  • Cleanly interrupting offline curation
  • Uploading contigs from the command line
• Definition downloads
  • Allele sequence definitions
    • Scheme tree
    • Alphabetical list
    • All loci by scheme
    • Download locus table
  • Scheme profile definitions
• Data records
  • Isolate records
    • Projects
    • Provenance metadata
    • Publications
    • Sequence bin summary
    • Scheme and locus data
  • Allele definition records
  • Sequence tag records
  • Profile records
  • Sequence bin records
• Querying data
  • Querying sequences to determine allele identity
    • Querying whole genome data
  • Querying multiple sequences to identify allele identities
  • Searching for specific allele definitions
    • General (all loci) sequence attribute search
    • Locus-specific sequence attribute search
  • Browsing scheme profile definitions
  • Querying scheme profile definitions
  • Identifying allelic profile definitions
  • Batch profile queries
  • Investigating allele differences
    • Sequence similarity
    • Sequence comparison
  • Browsing isolate data
  • Querying isolate data
    • Query by allele designation/scheme field
    • Query by allele designation count
    • Query by allele designation status
    • Query by sequence tag count
    • Query by tagged sequence status
    • Query by list of attributes
    • Query filters
  • Querying by allelic profile
  • Retrieving isolates by linked publication
  • User-configurable options
    • General options
    • Main results table
    • Isolate record display
    • Provenance field display
    • Query filters
    • Modifying locus and scheme display options
• User projects
  • Adding isolates to a user project following a query
  • Adding or removing isolates belonging to a user project by editing a list
  • Accessing project isolates
  • Allowing other users to share your project
  • Deleting a user project
• Private records
  • Uploading private records
  • Modifying private records
  • Sharing access to private records
• Data analysis plugins
  • Locus explorer
    • Polymorphic site analysis
    • Codon usage
    • Aligned translations
  • Field breakdown
  • Two field breakdown
  • Scheme and allele breakdown
  • Sequence bin breakdown
  • Genome comparator
    • Analysis using defined loci
    • Analysis using annotated reference genome
    • Include in identifiers fieldset
    • Reference genome fieldset
    • Parameters/options fieldset
    • Distance matrix calculation fieldset
    • Alignments fieldset
    • Core genome analysis fieldset
    • Filter fieldset
    • Understanding the output
      • Distance matrix
      • Unique strains
  • BLAST
    • Include in results table fieldset
    • Parameters fieldset
    • No matches
    • Filter fieldset
  • BURST
  • Codon usage
  • Unique combinations
  • Polymorphisms
  • Presence/absence
    • Options
  • Tag status
  • GrapeTree
• Data export plugins
  • Isolate record export
    • Advanced options
    • Molecular weight calculation
  • Sequence export
    • Aligning sequences
  • Profile export
  • Contig export
    • Filtering by tagged status of contigs
• Submitting data using the submission system
  • Registering a user account
  • Allele submission
    • Start
    • Select the submission locus
    • Enter details of sequencing method
    • Paste in sequence(s)
    • Add message to curator
    • Add supporting files
    • Finalize submission
  • Profile submission
    • Start
    • Paste in profile(s)
    • Add message to curator
    • Add supporting files
    • Finalize submission
  • Isolate submission
    • Start
    • Paste in isolate data
    • Add message to curator
    • Add supporting files
    • Finalize submission
  • Genome submission
  • Removing submissions from your notification list
• RESTful Application Programming Interface (API)
  • Passing additional/optional parameters
  • Paging using request headers
  • Resources
    • GET / or /db - List site resources
    • GET /db/{database} - List database resources
    • GET /db/{database}/classification_schemes - List classification schemes
    • GET /db/{database}/classification_schemes/{classification_scheme_id} - Retrieve classification scheme information and groups
    • GET /db/{database}/classification_schemes/{classification_scheme_id}/groups/{group_id} - List isolates belonging to a classification scheme group
    • 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
    • POST /db/{database}/loci/{locus}/sequence - Query sequence to identify allele
    • POST /db/{database}/sequence - Query sequence to identify allele without specifying locus
    • GET /db/{database}/schemes - List schemes
    • GET /db/{database}/schemes/{scheme_id} - Retrieve scheme information
    • GET /db/{database}/schemes/{scheme_id}/loci - Retrieve scheme loci
    • 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
    • POST /db/{database}/schemes/{scheme_id}/sequence - Query sequence to extract allele designations/fields for a scheme
    • 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}/isolates/{isolate_id}/history - Retrieve isolate update history
    • POST /db/{database}/isolates/search - Search isolate database
    • GET /db/{database}/contigs/{contig_id} - Retrieve contig record
    • GET /db/{database}/fields - Retrieve list of isolate provenance field descriptions
    • GET /db/{database}/fields/{field} - Retrieve values set for a provenance field
    • 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
    • Developer sign up to get a consumer key
    • Getting a request token
    • Getting user authorization
    • Getting an access token
    • Getting a session token
    • Accessing protected resources
• Frequently asked questions (FAQs)
  • General
  • Installation
  • Administration
• Appendix
  • Query operators
  • Sequence tag flags
  • Allele sequence flags
• Database schema