The Sequence Read Archive

By Rasko Leinonen, H. Sugawara, Martin Shumway. Nucleic Acids Res., 2010

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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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/83b2e0d77f3d7c4a2f296856fb09a68a1e097f13

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Citations in the corpus

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024 (2023, methodology): “Furthermore, CNCB-NGDC has established close collaborations with the International Nucleotide Sequence Database Collaboration (INSDC) ( 23 ) by mirroring the metadata and sequence data from NCBI SRA (Sequence Read Archive) ( 24 ).”
CircNet: a database of circular RNAs derived from transcriptome sequencing data (2015, methodology): “In addition, 464 RNA-seq samples were collected from a wide range of independent experiments across 26 human tissues and 104 disease conditions from the NCBI Sequence Read Archive (36).”
BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA (2023, neutral): “The RNA-seq data can be provided in three different forms: IDs of libraries available at the Sequence Read Archive (Leinonen et al., 2010), unaligned reads or aligned reads.”
Genomes OnLine Database (GOLD) v.8: overview and updates (2020, methodology): “There are three different ways in which projects and their associated metadata are entered into GOLD: (i) projects that are added by individual GOLD users; (ii) projects for samples sequenced at the Joint Genome Institute (JGI) as part of the JGI User Programs and (iii) projects sourced from public ”
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database (2020, positive): “RNA-seq data used in runs of BRAKER1 was sampled from the Sequence Read Archive (35) by VARUS (36).”