The ensembl analysis pipeline

被引：75

作者：

Potter, SC

Clarke, L

Curwen, V

Keenan, S

Mongin, E

Searle, SMJ

Stabenau, A

Storey, R

Clamp, M

机构：

[1] Wellcome Trust Sanger Inst, Cambridge CB10 1SD, England

[2] Wellcome Trust Sanger Inst, Cambridge CB10 1SD, England

[3] EMBL European Bioinformat Inst, Cambridge CB10 1SD, England

[4] Broad Inst, Cambridge, MA 02141 USA

来源：

GENOME RESEARCH | 2004年 / 14卷 / 05期

关键词：

D O I：

10.1101/gr.1859804

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：934 / 941

页数：8