GBrowse has a flexible adaptor (yes, it is spelled that way and is not “adapter”) system for running off various types of databases/sources. A common question is “which adaptor should I be using?” This attempts to answer that question.
| Adaptor | Other required software | Roughly how many users | Pros | Cons | |—-|—-|—-|—-|—-| | Bio::DB::SeqFeature::Store (use bp_seqfeature_load.pl) | MySQL, PostgreSQL, SQLite, BerkeleyDB | Many and growing fast. | Roughly 4X faster than Bio::DB::GFF for the same data; designed to work with GFF3 | Developed for use with GFF3; about 2X slower than Bio::DB::GFF to load a database | | Bio::DB::GFF (use bp_load_gff.pl, bp_bulk_load_gff.pl, bp_fast_load_gff.pl) | A relational database server: MySQL, PostgreSQL, Oracle, or BerkeleyDB | Lots! (Especially MySQL) | Quite fast; large user base; Have to use this if your data is in the (now deprecated) GFF2 format. | Does not work well with GFF3 formatted data | | Bio::DB::Sam (available from CPAN) | SAMtools | Growing (particularly with GBrowse2) | Very fast access to NextGen sequencing data | Difficult to use with GBrowse 1.70 | | Bio::DB::BigWig and Bio::DB::BigWigSet (available from CPAN) | UCSC Formats | Growing (particularly with GBrowse2) | Very fast access to data in bigWig format | Difficult to use with GBrowse 1.70 | | Bio::DB::BigBed (available from CPAN) | UCSC Formats | Growing (particularly with GBrowse2) | Very fast access to data in bigBed format | Difficult to use with GBrowse 1.70 | | Bio::DB::Das::Chado (available from CPAN) | PostgreSQL and a Chado schema | Relatively few due to the specialized nature of Chado | Allows ‘live’ viewing of the features in a Chado database | Slow compared to Bio::DB::GFF | | Bio::DB::Das::BioSQL (available from CPAN) | MySQL and a BioSQL schema | Relatively few due to the small number of BioSQL users | Allows ‘live’ viewing of the features in a BioSQL database | Slow compared to Bio::DB::GFF | | Memory (ie, flat file database using either Bio::DB::GFF or SeqFeature::Store) | None | For real servers, none | Easy for rapid development and testing | Very slow for more than a few thousand features | | LuceGene | Lucene (searches indexed flat files) | Relatively few | | |
There have been some useful email threads on adaptor choices and tradeoffs.