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Protocols

SRA specifications

Information


Unique identifier OMICS_01031
Name SRA
Alternative names Sequence Read Archive, SRA2R, NCBI SRA
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Sequence_Read_Archive

Documentation


Additional information


SRA2R, allows to import SRA data directly into R: https://github.com/NCBI-Hackathons/SRA2R

Publications for Sequence Read Archive

library_books

The Sequence Read Archive

2011 Nucleic Acids Res
PMCID: 3013647
PMID: 21062823
DOI: 10.1093/nar/gkq1019

SRA citations

 (1586)
library_books

Chitinase genes (CHIAs) provide genomic footprints of a post Cretaceous dietary radiation in placental mammals

2018
Sci Adv
PMCID: 5955627
PMID: 29774238
DOI: 10.1126/sciadv.aar6478

[…] e species that have (T. chinensis) or potentially have (M. californicus and Desmodus rotundus) three or more CHIAs in their genomes (tables S1 and S3). These libraries have been deposited into NCBI’s Sequence Read Archive, so we queried them via NCBI’s BLAST interface. We BLASTed (megablast) all five of the assembled T. chinensis CHIA paralogs against a pancreas library (). M. californicus and D. […]

library_books

Methionine metabolism influences genomic architecture and gene expression through H3K4me3 peak width

2018
Nat Commun
PMCID: 5955993
PMID: 29769529
DOI: 10.1038/s41467-018-04426-y

[…] for mouse liver using Bowtie2, and filtered according to alignment scores using SAMtools. SRA files were converted to FASTQ format using the command fastq-dump in the SRA Toolkit (https://github.com/ncbi/sra-tools) before the alignment. Peaks were called using MACS2 without the --broad option and filtered with the criterion that the enrichment Q-value is smaller than 10−5. H3K4me3 peaks bound by […]

call_split

Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer

2018
mSystems
PMCID: 5954203
DOI: 10.1128/mSystems.00205-17
call_split See protocol

[…] The 16S rRNA gene sequencing data were previously published (). Raw sequences were deposited in the NCBI Sequence Read Archive under project accession number PRJNA284355, and processed data files are available in the work of Burns et al. (). Briefly, total DNA was extracted from approximately 100 mg of t […]

library_books

Diversity and antimicrobial potential in sea anemone and holothurian microbiomes

2018
PLoS One
PMCID: 5942802
PMID: 29742123
DOI: 10.1371/journal.pone.0196178

[…] used to chimera removal. The unassigned OTUs obtained were assigned using RDP’s Classifier [] release 11.4 (May 26, 2015). The FASTQ files generated after the metagenome sequencing were deposited in Sequence Read Archive database (SRA-NCBI; https://www.ncbi.nlm.nih.gov/sra), with the BioProject ID PRJNA420053 and BioSample accession numbers from SAMN08104840 to SAMN08104849. […]

call_split

Genetic diversity and virulence profiles of Listeria monocytogenes recovered from bulk tank milk, milk filters, and milking equipment from dairies in the USA (2002 to 2014)

2018
PLoS One
PMCID: 5942804
PMID: 29742151
DOI: 10.1371/journal.pone.0197053
call_split See protocol

[…] nomes were sequenced by using 250-bp paired-end libraries, with a MiSeq reagent kit (v2), on a MiSeq system (Illumina), per the manufacturer's instructions. Raw sequencing reads were deposited in the NCBI SRA database under BioProject PRJNA215355 (Listeria monocytogenes database, US Food and Drug Administration GenomeTrakr Project) (). Sequencing contaminants were trimmed and removed using Trimmom […]

library_books

Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis

2018
BMC Genomics
PMCID: 5954272
PMID: 29764361
DOI: 10.1186/s12864-018-4456-9

[…] The data analysis process of this research is summarized in Fig. . First, to identify circRNA, transcriptome sequencing data sets were obtained from the NCBI Sequence Read Archive (SRA). The back-spliced junction sites in each RNA-seq sample were identified using a circRNA discovery pipeline adapting the scripts provided on circBase [, ], which was referre […]

Citations

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SRA institution(s)
Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima, Japan; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA; European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
SRA funding source(s)
Supported by the DNA Data Bank of Japan, Ministry of Education, Culture, Sports, Science and Technology of Japan, the European Molecular Biology Laboratory, the European Commission and the Wellcome Trust, the National Library of Medicine, and Intramural Research Program of the NIH.

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