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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://usm69b.wcbzw.com/.

  • Concepts and terms
    • BIGSdb
    • Loci
    • Alleles
    • Schemes
    • Profiles
    • Classification groups
    • Sequence tags
    • Sets
  • BIGSdb dependencies
    • Required packages
  • Installation and configuration of BIGSdb
    • Software installation
    • Configuring PostgreSQL
    • 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
    • Log file rotation
    • Upgrading BIGSdb
    • Running the BIGSdb RESTful interface
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    • Creating databases
    • Database-specific configuration
    • XML configuration attributes used in config.xml
    • Over-riding global defaults set in bigsdb.conf
    • Over-riding values set in config.xml
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    • Sparsely-populated fields
    • Kiosk mode
    • User authentication
    • Setting up the admin user
    • Retrieving PubMed citations from NCBI
    • Configuring access to remote contigs
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    • 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
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    • Improving performance
    • Dataset partitioning
    • Setting a site-wide users database
    • 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
    • Automated assignment of scheme profiles
    • Scheme profile clustering - setting up classification schemes
    • 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
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    • BLAST caches
    • Config-specific file downloads
  • 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
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    • 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
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    • Linking remote contigs to isolate records
    • Automated web-based sequence tagging
    • Projects
    • Isolate record versioning
  • Curating data submitted via the automated submission system
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    • Profiles
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  • 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 profile definitions
  • Data records
    • Isolate records
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    • Sequence tag records
    • Profile records
    • Sequence bin records
  • Querying data
    • Querying sequences to determine allele identity
    • Querying multiple sequences to identify allele identities
    • Searching for specific allele definitions
    • Browsing scheme profile definitions
    • Querying scheme profile definitions
    • Identifying allelic profile definitions
    • Batch profile queries
    • Investigating allele differences
    • Browsing isolate data
    • Querying isolate data
    • Querying by allelic profile
    • Retrieving isolates by linked publication
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  • 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
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    • BLAST
    • BURST
    • Codon usage
    • Field breakdown
    • Gene Presence
    • Genome comparator
    • GrapeTree
    • In silico PCR
    • Interactive Tree of Life (iTOL)
    • Locus explorer
    • Microreact
    • PhyloViz
    • Polymorphisms
    • Species identification
    • Sequence bin breakdown
    • Two field breakdown
    • Unique combinations
  • Data export plugins
    • Contig export
    • Isolate record export
    • Profile export
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  • Submitting data using the submission system
    • Registering a user account
    • Allele submission
    • Profile submission
    • Isolate submission
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    • Removing submissions from your notification list
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    • Passing additional/optional parameters
    • Paging using request headers
    • Resources
    • Authentication
  • Frequently asked questions (FAQs)
    • General
    • Installation
    • Administration
  • Appendix
    • Query operators
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    • Allele sequence flags
  • Database schema