# The NCBI SRA (Sequence Read Archive)

### Contact:
email: sra@ncbi.nlm.nih.gov

### Download
Visit our [download page](https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit) 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](https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump).

For additional information on using, configuring, and building the toolkit,
please visit our [wiki](https://github.com/ncbi/sra-tools/wiki)
or our web site at [NCBI](http://www.ncbi.nlm.nih.gov/Traces/sra/?view=toolkit_doc)


SRA Toolkit Development Team