enformatik / sra-tools

SRA Tools

The NCBI SRA (Sequence Read Archive)

Contact:

email: [email protected]

Download

Visit our download page for pre-built binaries.

Change Log

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.

ANNOUNCEMENT:

SRA Toolkit 2.10.5 sratools: fixed a potential build problem in libutf8proc ncbi-vdb, ngs, ngs-tools, sra-tools: all Linux builds now use g++ 7.3 (C++11 ABI) prefetch: improvements were made to work in environments with bad network connections prefetch, sratools: fixed the names of the --min-size and --max-size command line arguments when running prefetch

SRA Toolkit 2.10.4 kns, sra-tools:: fixed errors when using ngc file

SRA Toolkit 2.10.3 sraxf, fasterq-dump, fastq-dump, sam-dump: fixed a problem resulting in a segmentation fault

Release 2.10.2 of sra-tools provides access to all the public and controlled-access dbGaP of SRA in the AWS and GCP environments (Linux only for this release). This vast archive's original submission format and SRA-formatted data can both be accessed and computed on these clouds, eliminating the need to download from NCBI FTP as well as improving performance.

The prefetch tool also retrieves original submission files in addition to ETL data for public and controlled-access dbGaP data.

With release 2.10.0 of sra-tools we have added cloud-native operation for AWS and GCP environments (Linux only for this release), for use with the public SRA. prefetch is capable of retrieving original submission files in addition to ETL data.

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.

For additional information on using, configuring, and building the toolkit, please visit our wiki or our web site at NCBI

SRA Toolkit Development Team