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Nucleic Acids Research Advance Access originally published online on October 31, 2008
Nucleic Acids Research 2009 37(Database issue):D19-D25; doi:10.1093/nar/gkn765
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Nucleic Acids Research, 2009, Vol. 37, Database issue D19-D25
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

Petabyte-scale innovations at the European Nucleotide Archive

Guy Cochrane1,*, Ruth Akhtar1, James Bonfield2, Lawrence Bower1, Fehmi Demiralp1, Nadeem Faruque1, Richard Gibson1, Gemma Hoad1, Tim Hubbard2, Christopher Hunter1, Mikyung Jang1, Szilveszter Juhos1, Rasko Leinonen1, Steven Leonard2, Quan Lin1, Rodrigo Lopez1, Dariusz Lorenc1, Hamish McWilliam1, Gaurab Mukherjee1, Sheila Plaister1, Rajesh Radhakrishnan1, Stephen Robinson1, Siamak Sobhany1, Petra Ten Hoopen1, Robert Vaughan1, Vadim Zalunin1 and Ewan Birney1

1EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 2Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

*To whom correspondence should be addressed. Tel: +44 (0) 1223 4925634; Fax: +44 (0) 1223 494 468; Email: cochrane{at}ebi.ac.uk

Received September 30, 2008. Revised October 3, 2008. Accepted October 6, 2008.

Dramatic increases in the throughput of nucleotide sequencing machines, and the promise of ever greater performance, have thrust bioinformatics into the era of petabyte-scale data sets. Sequence repositories, which provide the feed for these data sets into the worldwide computational infrastructure, are challenged by the impact of these data volumes. The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/embl), comprising the EMBL Nucleotide Sequence Database and the Ensembl Trace Archive, has identified challenges in the storage, movement, analysis, interpretation and visualization of petabyte-scale data sets. We present here our new repository for next generation sequence data, a brief summary of contents of the ENA and provide details of major developments to submission pipelines, high-throughput rule-based validation infrastructure and data integration approaches.


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