The Ensembl Analysis Pipeline

  1. Simon C. Potter1,
  2. Laura Clarke1,
  3. Val Curwen1,
  4. Stephen Keenan1,
  5. Emmanuel Mongin2,
  6. Stephen M.J. Searle1,
  7. Arne Stabenau2,
  8. Roy Storey1, and
  9. Michele Clamp3,4
  1. 1 The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
  2. 2 EMBL European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
  3. 3 The Broad Institute, Cambridge, Massachusetts 02141, USA

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.

Footnotes

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1859804.

  • ↵4 Corresponding author. E-MAIL mclamp{at}broad.mit.edu; FAX (617) 258-0903.

    • Accepted January 12, 2004.
    • Received August 8, 2003.
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  1. doi: 10.1101/gr.1859804 Genome Res. 14: 934-941 Cold Spring Harbor Laboratory Press

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