The sequence read archive
- PMID: 21062823
- PMCID: PMC3013647
- DOI: 10.1093/nar/gkq1019
The sequence read archive
Abstract
The combination of significantly lower cost and increased speed of sequencing has resulted in an explosive growth of data submitted into the primary next-generation sequence data archive, the Sequence Read Archive (SRA). The preservation of experimental data is an important part of the scientific record, and increasing numbers of journals and funding agencies require that next-generation sequence data are deposited into the SRA. The SRA was established as a public repository for the next-generation sequence data and is operated by the International Nucleotide Sequence Database Collaboration (INSDC). INSDC partners include 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 http://www.ncbi.nlm.nih.gov/Traces/sra from NCBI, at http://www.ebi.ac.uk/ena from EBI and at http://trace.ddbj.nig.ac.jp from DDBJ. In this article, we present the content and structure of the SRA, detail our support for sequencing platforms and provide recommended data submission levels and formats. We also briefly outline our response to the challenge of data growth.
Similar articles
-
The Sequence Read Archive: explosive growth of sequencing data.Nucleic Acids Res. 2012 Jan;40(Database issue):D54-6. doi: 10.1093/nar/gkr854. Epub 2011 Oct 18. Nucleic Acids Res. 2012. PMID: 22009675 Free PMC article.
-
Archiving next generation sequencing data.Nucleic Acids Res. 2010 Jan;38(Database issue):D870-1. doi: 10.1093/nar/gkp1078. Epub 2009 Dec 3. Nucleic Acids Res. 2010. PMID: 19965774 Free PMC article.
-
DDBJ new system and service refactoring.Nucleic Acids Res. 2013 Jan;41(Database issue):D25-9. doi: 10.1093/nar/gks1152. Epub 2012 Nov 24. Nucleic Acids Res. 2013. PMID: 23180790 Free PMC article.
-
The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments.Nucleic Acids Res. 2012 Jan;40(Database issue):D38-42. doi: 10.1093/nar/gkr994. Epub 2011 Nov 22. Nucleic Acids Res. 2012. PMID: 22110025 Free PMC article.
-
Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format.Patterns (N Y). 2022 Sep 9;3(9):100562. doi: 10.1016/j.patter.2022.100562. Epub 2022 Jul 7. Patterns (N Y). 2022. PMID: 35818472 Free PMC article. Review.
Cited by
-
Unraveling the evolutionary trajectory of LHCI in red-lineage algae: Conservation, diversification, and neolocalization.iScience. 2024 Sep 13;27(10):110897. doi: 10.1016/j.isci.2024.110897. eCollection 2024 Oct 18. iScience. 2024. PMID: 39386759 Free PMC article.
-
RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing.PeerJ. 2024 Sep 25;12:e17893. doi: 10.7717/peerj.17893. eCollection 2024. PeerJ. 2024. PMID: 39346055 Free PMC article.
-
VMAP: Vaginal Microbiome Atlas during Pregnancy.JAMIA Open. 2024 Sep 27;7(3):ooae099. doi: 10.1093/jamiaopen/ooae099. eCollection 2024 Oct. JAMIA Open. 2024. PMID: 39345789 Free PMC article.
-
FEAtl: a comprehensive web-based expression atlas for functional genomics in tropical and subtropical fruit crops.BMC Plant Biol. 2024 Sep 30;24(1):890. doi: 10.1186/s12870-024-05595-3. BMC Plant Biol. 2024. PMID: 39343895 Free PMC article.
-
Characterization of Neutrophil Functional Responses to SARS-CoV-2 Infection in a Translational Feline Model for COVID-19.Int J Mol Sci. 2024 Sep 19;25(18):10054. doi: 10.3390/ijms251810054. Int J Mol Sci. 2024. PMID: 39337543 Free PMC article.
References
Publication types
MeSH terms
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources