title: The Ensembl analysis pipeline.
abstract: The Ensembl pipeline is an extension to the Ensembl system which allows automated annotation of genomic sequence. The software comprises two parts. First, there is a set of Perl modules ("Runnables" and "RunnableDBs") which are 'wrappers' for a variety of commonly used analysis tools. These retrieve sequence data from a relational database, run the analysis, and write the results back to the database. They inherit from a common interface, which simplifies the writing of new wrapper modules. On top of this sits a job submission system (the "RuleManager") which allows efficient and reliable submission of large numbers of jobs to a compute farm. Here we describe the fundamental software components of the pipeline, and we also highlight some features of the Sanger installation which were necessary to enable the pipeline to scale to whole-genome analysis.
authors.affiliation: The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Simon C
authors.initials: SC
authors.lastname: Potter
authors.forename: Laura
authors.initials: L
authors.lastname: Clarke
authors.forename: Val
authors.initials: V
authors.lastname: Curwen
authors.forename: Stephen
authors.initials: S
authors.lastname: Keenan
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Mongin
authors.forename: Stephen M J
authors.initials: SM
authors.lastname: Searle
authors.forename: Arne
authors.initials: A
authors.lastname: Stabenau
authors.forename: Roy
authors.initials: R
authors.lastname: Storey
authors.forename: Michele
authors.initials: M
authors.lastname: Clamp
mesh_terms: D001483:Base Sequence / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000235:genetics; D030541:Databases, Genetic / Q000592:standards; D011381:Programming Languages; D011506:Proteins / Q000145:classification; D012984:Software; D012985:Software Design
chemical_list: D011506:Proteins; D004247:DNA