• Statistical tools for data analysis and visualization.
• Researchers commonly use SRA data to make discoveries via comparison of data sets. Data sets can be compared through the SRA web interface, but if you want to integrate these downloads and file conversions into an already existing pipeline, or you simply prefer using a command-line interface, we recommend using 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. By data scientists, for data scientists.

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The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

Much of the data submitted these days contain alignment information, for example in BAM, Illumina export.txt, and Complete Genomics formats. With aligned data, NCBI uses Compression by Reference, which only stores the differences in base pairs between sequence data and the segment it aligns to. The process to restore original data, for example as FastQ, requires fast access to the reference sequences that the original data was aligned to. NCBI recommends that SRA users dedicate local disk space to store references downloaded from the NCBI SRA site. As of February 2015, the complete collection of these reference sequences is 98 GB. While it isn't usually necessary to download the entirety of the reference sequences, this should give you an idea of the scale of the storage requirement. By default, the Toolkit will download missing reference sequences on demand and cache them in the user's home directory. The location of this cache is configurable, as is whether the download is automatic or manual.

Use Sra Toolkit

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

SRA Toolkit Development Team

How To Use Sra Toolkit

Daler / packages / sratoolkit 2.5.72. The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. License: Public Domain. 4551 total downloads. Last upload: 5 years and 4 months ago. In some cases, users may want to download SRA data and retain a copy. To download using NCBI's 'prefetch' tool, you would need to set up your own configuration file for the NCBI SRA toolkit. Use the command vdb-config to set up a directory for downloading. In the following example, the vdb-config utility is used to set up /data/$USER/sra-data as the local repository for downloading SRA data. Remember that /home/$USER is limited to a quota of 16 GB, so it is best to direct your downloaded SRA.