The NCBI SRA (Sequence Read Archive)
Visit our download page for pre-built binaries.
Please check the CHANGES.md file for change history.
The 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.
With release 2.9.1 of
sra-tools we have finally made available the tool
fasterq-dump, a replacement for the much older
fastq-dump tool. As its name implies, it runs faster, and is better suited for large-scale conversion of SRA objects into FASTQ files that are common on sites with enough disk space for temporary files.
fasterq-dump is multi-threaded and performs bulk joins in a way that improves performance as compared to
fastq-dump, which performs joins on a per-record basis (and is single-threaded).
fastq-dump is still supported as it handles more corner cases than
fasterq-dump, but it is likely to be deprecated in the future.
You can get more information about
fasterq-dump in our Wiki at https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump.
As was announced in OMB memorandum M-15-13 on June 8, 2015, NCBI and all Federal systems will be transitioning to using HTTPS-only protocols before the end of 2016. This change will affect any software that uses NCBI APIs such as the E-utilities or NCBI software toolkits such as
The NLM and NCBI may implement the switch to HTTPS-only as early as September 30, 2016.
In particular, software products that depend on
ngs may not function as expected after September 30 unless they are properly updated from this site or by the software provider.
If you use software that accesses NCBI SRA data in any way, your software will likely be affected by this change. Please check with your software provider for recent udpates or patches, and be sure to acquire these before September 30.
If you develop software that relies on
ngs in any way, you will likely need to update your code so that it accesses NCBI using HTTPS.
We have released new tools with version 2.8.0 that are HTTPS compatible and
M-15-13 compliant as of October 7, 2016. Please be certain to update all of your binaries and configuration files.
SRA Toolkit Development Team