NCBI SRA overview
The Sequence Read Archive (SRA), established by the National Institutes of Health (NIH), represents a cornerstone of modern genomic research as the world’s preeminent publicly available repository for high-throughput sequencing data. SRA stores raw sequencing data and alignment information to enhance reproducibility and facilitate discoveries through data analysis. As an integral component of the International Nucleotide Sequence Database Collaboration (INSDC), the SRA operates through a sophisticated tripartite alliance between the NCBI Sequence Read Archive, the European Bioinformatics Institute (EBI), and the DNA Database of Japan (DDBJ), ensuring seamless global data sharing and accessibility.
This archive accommodates raw sequencing data and alignment information across all branches of life, including metagenomic and environmental surveys, while maintaining stringent protocols for data integrity, particularly in handling clinically sensitive human subject data through controlled-access mechanisms.
NCBI SRA Toolkit
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. The SRA Toolkit provides 64-bit binary installations for the Ubuntu and CentOS Linux distributions, for Mac OS X, and for Windows.
| Windows | sratoolkit.current-win64.zip |
| Ubuntu | sratoolkit.current-ubuntu64.tar.gz |
| CentOS | sratoolkit.current-centos_linux64.tar.gz |
| Mac OS X | sratoolkit.current-mac64.tar.gz |
SRA Toolkit
| Source code | GitHub repository |
| Current version | 3.1.1 |
| Operating system | Linux, macOS, Windows |
| Software interface | Command-line interface |
| Input Data formats | SRA format |
| Output Data formats | FASTQ, SAM, BAM |
| Dependencies | None (self-contained) |
| Standalone tools | fastq-dump, prefetch, fasterq-dump, sam-dump, vdb-config |
| Supported technologies | All SRA-stored sequencing data |
| Availability | Free and open-source |
| Maintained and Supported by | NCBI/NIH |
| License | Public Domain |
Feedback and bug reports
Please, leave your comments and bug reports at GitHub repository or email: sra@ncbi.nlm.nih.gov
Citation and usage
NCBI Sequence Read Archive Toolkit. National Center for Biotechnology Information. Available from: https://github.com/ncbi/sra-tools
This information is provided for educational and research purposes only. There is no affiliation, endorsement, or partnership with the tool developers or associated institutions.
