Sequence Read Archive

Abbreviation:SRA

Recommended

General Information

The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.

Homepage http://www.ncbi.nlm.nih.gov/sra

Developed in United States

Created in 2007

Taxonomic range

Scope and data types

Nucleic acid sequence alignment

Nucleotide

Sequence

Sequence alignment

In the following recommendations:

How to cite this record FAIRsharing.org: SRA; Sequence Read Archive; DOI: https://doi.org/10.25504/FAIRsharing.g7t2hv; Last edited: Aug. 22, 2018, 12:31 p.m.; Last accessed: Sep 20 2018 11:17 p.m.

Record updated: July 26, 2018, 6:49 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.g7t2hv' by 'The FAIRsharing Team' at 18:49, 26 Jul 2018 (approved):

	'domains' has been modified:
		Before:
			Life Science
			Sequence
		After:
			Allele
			DNA sequence
			DNA sequence data
			Gene
			Life Science
			Nucleic acid sequence alignment
			Nucleotide
			Sequence
			Sequence alignment
		Added:
			Allele
			DNA sequence
			DNA sequence data
			Gene
			Nucleic acid sequence alignment
			Nucleotide
			Sequence alignment
		Removed:

	'contact' has been modified:
		Before: 
		After: General Contact

	'tools' has been modified:
		Before:
			BLAST||http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&BLAST_SPEC=SRA&SHOW_DEFAULTS=on
			submit||http://www.ncbi.nlm.nih.gov/Traces/sra_sub/sub.cgi
		After:
			BLAST||http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&BLAST_SPEC=SRA&SHOW_DEFAULTS=on
		Added:
		Removed:
			submit||http://www.ncbi.nlm.nih.gov/Traces/sra_sub/sub.cgi

	'publications' has been modified:
		Before:
			The Sequence Read Archive: explosive growth of sequencing data.|Kodama Y., Shumway M., Leinonen R., |Nucleic Acids Res.|2012
			Database resources of the National Center for Biotechnology Information|Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Ostell J, Pruitt KD, Schuler GD, Shumway M, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E.|Nucleic Acids Res.|2008
		After:
			The Sequence Read Archive: explosive growth of sequencing data.|Kodama Y., Shumway M., Leinonen R., |Nucleic Acids Res.|2012
			Database resources of the National Center for Biotechnology Information|Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Ostell J, Pruitt KD, Schuler GD, Shumway M, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E.|Nucleic Acids Res.|2008
			Investigation into the annotation of protocol sequencing steps in the sequence read archive.|Alnasir J,Shanahan HP|Gigascience|2015
		Added:
			Investigation into the annotation of protocol sequencing steps in the sequence read archive.|Alnasir J,Shanahan HP|Gigascience|2015
		Removed:

	'dataProcesses' has been modified:
		Before:
			Download
		After:
			Download
			Submit
			Browse
			Search
		Added:
			Submit
			Browse
			Search
		Removed:

In Collections

Data Citation Implementation

Open Science Prize

NIH-supported data repositories

Wheat Data Interoperability Guidelines

Support

General

contact form	http://www.ncbi.nlm.nih.gov/Traces/sra/s ...
help	http://www.ncbi.nlm.nih.gov/books/NBK475 ...
Mailing List	None
online documentation	http://www.ncbi.nlm.nih.gov/Traces/sra
online documentation	http://www.ncbi.nlm.nih.gov/Traces/sra/s ...
training	http://www.ncbi.nlm.nih.gov/Traces/sra_s ...

Additional Information

Contact	General Contact
Identifiers.org	MIR:00000243

Tools

BLAST

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS= ...

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Attribution required
Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0

Data Access

Download	http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=download_reads
Submit	http://www.ncbi.nlm.nih.gov/Traces/sra_sub/sub.cgi
Browse	https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=run_browser
Search	https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=search_obj

Publications

The Sequence Read Archive: explosive growth of sequencing data.

Kodama Y., Shumway M., Leinonen R.,
Nucleic Acids Res. 2012

View Paper (PubMed)

Database resources of the National Center for Biotechnology Information

Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Ostell J, Pruitt KD, Schuler GD, Shumway M, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E.
Nucleic Acids Res. 2008

View Paper (PubMed)

Investigation into the annotation of protocol sequencing steps in the sequence read archive.

Alnasir J,Shanahan HP
Gigascience 2015

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

Terminology Artifacts

No semantic standards defined

Models and Formats

Short Read Archive eXtensible Markup Language

Related Databases

Implementing Policies

Credit

Record Maintainer

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Maintains

National Center for Biotechnology Information (NCBI), Rockville, MD, USA (Research institute)

Sequence Read Archive

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