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The NCBI SRA ( Sequence Read Archive )


Contact: sra-tools@ncbi.nlm.nih.gov
http://trace.ncbi.nlm.nih.gov/Traces/sra/std

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

With this release, NCBI has implemented Compression by Reference, a
sequence alignment compression process for storing sequence data.
Currently BAM, Complete Genomics and Illumina export.txt formats
contain alignment information. Compression by Reference only stores
the difference in base pairs between sequence data and the segments it
aligns to.  The decompression process to restore original data such as
fastq-dump would require fast access to the actual sequences of the
references. NCBI recommends that SRA users dedicate local disk space
to store local references downloaded from the NCBI SRA site. Linked
references should be in a location accessible by the SRA Reader
software.

Older files in the NCBI system may not have been compressed using
Compression by Reference.  For more information on how to use
Reference-based compressed files, download local references, and use
related tools please refer to Compression by Reference file on the
NCBI SRA website:

    "http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=softwareReadme"


For additional information on using and building the toolkit,
please visit our web site at:

    "http://trace.ncbi.nlm.nih.gov/Traces/sra/std"


SRA Toolkit Development Team
