SRAdb

Package: SRAdb
Type: Package
Title: A compilation of metadata from NCBI SRA and tools
Version: 1.35.0
Date: 2016-04-28
Depends: RSQLite, graph, RCurl
Imports: GEOquery
Suggests: Rgraphviz
Author: Jack Zhu and Sean Davis
Maintainer: Jack Zhu <zhujack@mail.nih.gov>
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.
License: Artistic-2.0
LazyLoad: yes
BugReports: https://github.com/seandavi/SRAdb/issues/new
biocViews: Infrastructure, Sequencing, DataImport

Raw database downloads

• sqlite3 (.gz)
• MySQL (mysqldump.gz)