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PubMed · 15123589

The Ensembl analysis pipeline.

Simon C Potter·Laura Clarke·Val Curwen·Stephen Keenan·Emmanuel Mongin·Stephen M J Searle·Arne Stabenau·Roy Storey·Michele Clamp
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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.

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Simon C Potter, Laura Clarke, Val Curwen, Stephen Keenan, Emmanuel Mongin, Stephen M J Searle, Arne Stabenau, Roy Storey, Michele Clamp. 2004. The Ensembl analysis pipeline.. https://doi.org/10.1101/gr.1859804

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