SRAdb: A compilation of metadata from NCBI SRA and tools

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SRAdb")
AuthorJack Zhu and Sean Davis
Bioconductor views DataImport Infrastructure Sequencing
Date of publicationNone
MaintainerJack Zhu <zhujack@mail.nih.gov>
LicenseArtistic-2.0
Version1.34.0
http://gbnci.abcc.ncifcrf.gov/sra/

View on Bioconductor

Functions

ascpR Man page
ascpSRA Man page
colDescriptions Man page
entityGraph Man page
getFASTQfile Man page
getFASTQinfo Man page
getSRA Man page
getSRAdbFile Man page
getSRAfile Man page
getSRAinfo Man page
IGVclear Man page
IGVcollapse Man page
IGVgenome Man page
IGVgoto Man page
IGVload Man page
IGVsession Man page
IGVsnapshot Man page
IGVsocket Man page
IGVsort Man page
listSRAfile Man page
sraConvert Man page
SRAdb Man page
SRAdb-package Man page
sraGraph Man page
startIGV Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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