A compilation of metadata from NCBI SRA and tools
Description
The Sequence Read Archive (SRA) is the largest public
repository of sequencing data from the next generation of
sequencing platforms including Roche 454 GS System, Illumina
Genome Analyzer, Applied Biosystems SOLiD System, Helicos
Heliscope, and others. However, finding data of interest can be
challenging using current tools. SRAdb is an attempt to make
access to the metadata associated with submission, study,
sample, experiment and run much more feasible. This is
accomplished by parsing all the NCBI SRA metadata into a SQLite
database that can be stored and queried locally. Fulltext
search in the package make querying metadata very flexible and
powerful. fastq and sra files can be downloaded for doing
alignment locally. Beside ftp protocol, the SRAdb has funcitons
supporting fastp protocol (ascp from Aspera Connect) for faster
downloading large data files over long distance. The SQLite
database is updated regularly as new data is added to SRA and
can be downloaded at will for the most up-to-date metadata.