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The sequence read archive: explosive growth of sequencing data

New generation sequencing platforms are producing data with significantly higher throughput and lower cost. A portion of this capacity is devoted to individual and community scientific projects. As these projects reach publication, raw sequencing datasets are submitted into the primary next-generati...

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Detalles Bibliográficos
Autores principales: Kodama, Yuichi, Shumway, Martin, Leinonen, Rasko
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245110/
https://www.ncbi.nlm.nih.gov/pubmed/22009675
http://dx.doi.org/10.1093/nar/gkr854
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author Kodama, Yuichi
Shumway, Martin
Leinonen, Rasko
author_facet Kodama, Yuichi
Shumway, Martin
Leinonen, Rasko
author_sort Kodama, Yuichi
collection PubMed
description New generation sequencing platforms are producing data with significantly higher throughput and lower cost. A portion of this capacity is devoted to individual and community scientific projects. As these projects reach publication, raw sequencing datasets are submitted into the primary next-generation sequence data archive, the Sequence Read Archive (SRA). Archiving experimental data is the key to the progress of reproducible science. The SRA was established as a public repository for next-generation sequence data as a part of the International Nucleotide Sequence Database Collaboration (INSDC). INSDC is composed of the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI) and the DNA Data Bank of Japan (DDBJ). The SRA is accessible at www.ncbi.nlm.nih.gov/sra from NCBI, at www.ebi.ac.uk/ena from EBI and at trace.ddbj.nig.ac.jp from DDBJ. In this article, we present the content and structure of the SRA and report on updated metadata structures, submission file formats and supported sequencing platforms. We also briefly outline our various responses to the challenge of explosive data growth.
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spelling pubmed-32451102012-01-10 The sequence read archive: explosive growth of sequencing data Kodama, Yuichi Shumway, Martin Leinonen, Rasko Nucleic Acids Res Articles New generation sequencing platforms are producing data with significantly higher throughput and lower cost. A portion of this capacity is devoted to individual and community scientific projects. As these projects reach publication, raw sequencing datasets are submitted into the primary next-generation sequence data archive, the Sequence Read Archive (SRA). Archiving experimental data is the key to the progress of reproducible science. The SRA was established as a public repository for next-generation sequence data as a part of the International Nucleotide Sequence Database Collaboration (INSDC). INSDC is composed of the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI) and the DNA Data Bank of Japan (DDBJ). The SRA is accessible at www.ncbi.nlm.nih.gov/sra from NCBI, at www.ebi.ac.uk/ena from EBI and at trace.ddbj.nig.ac.jp from DDBJ. In this article, we present the content and structure of the SRA and report on updated metadata structures, submission file formats and supported sequencing platforms. We also briefly outline our various responses to the challenge of explosive data growth. Oxford University Press 2012-01 2011-10-18 /pmc/articles/PMC3245110/ /pubmed/22009675 http://dx.doi.org/10.1093/nar/gkr854 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Kodama, Yuichi
Shumway, Martin
Leinonen, Rasko
The sequence read archive: explosive growth of sequencing data
title The sequence read archive: explosive growth of sequencing data
title_full The sequence read archive: explosive growth of sequencing data
title_fullStr The sequence read archive: explosive growth of sequencing data
title_full_unstemmed The sequence read archive: explosive growth of sequencing data
title_short The sequence read archive: explosive growth of sequencing data
title_sort sequence read archive: explosive growth of sequencing data
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245110/
https://www.ncbi.nlm.nih.gov/pubmed/22009675
http://dx.doi.org/10.1093/nar/gkr854
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