SRAdb: A compilation of metadata from NCBI SRA and tools

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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.

Author
Jack Zhu and Sean Davis
Date of publication
None
Maintainer
Jack Zhu <zhujack@mail.nih.gov>
License
Artistic-2.0
Version
1.32.0
URLs

View on Bioconductor

Man pages

ascpR
Fasp file downloading using the ascp command line program
ascpSRA
Fasp SRA data file downloading using the ascp command line...
colDescriptions
Get column descriptions of SRAmetadb.sqlite
entityGraph
Create a new graphNEL object from an input entity matrix or...
getFASTQfile
Download SRA fastq files from EBI ENA through ftp or fasp
getFASTQinfo
Get SRA fastq file information and associated meta data from...
getSRA
Fulltext search SRA meta data using SQLite fts3 module
getSRAdbFile
Download and unzip last version of SRAmetadb.sqlite.gz from...
getSRAfile
Download SRA data file through ftp or fasp
getSRAinfo
Get SRA data file information from NCBI SRA
IGVclear
Clear IGV tracks loaded.
IGVcollapse
Collapse tracks in the IGV
IGVgenome
Set the IGV genome.
IGVgoto
Go to a specified region in IGV.
IGVload
Load data into IGV via remote port call.
IGVsession
Create an IGV session file
IGVsnapshot
Make a file snapshot of the current IGV screen.
IGVsocket
Create a Socket Connection to IGV.
IGVsort
Sort an alignment track by the specified option.
listSRAfile
List sra, sra-lite or fastq data file names associated with...
sraConvert
Cross-reference between GEO data types
SRAdb-package
Query NCBI SRA metadata within R or from a local SQLite...
sraGraph
Create a new graphNEL object of SRA accessios from SRA full...
startIGV
Start IGV from R with different amount maximum memory support

Files in this package

SRAdb/.BBSoptions
SRAdb/DESCRIPTION
SRAdb/NAMESPACE
SRAdb/NEWS
SRAdb/R
SRAdb/R/IGVapi.R
SRAdb/R/IGVsession.R
SRAdb/R/SRAdb-internal.R
SRAdb/R/ascpR.R
SRAdb/R/ascpSRA.R
SRAdb/R/colDescriptions.R
SRAdb/R/entityGraph.R
SRAdb/R/getFASTQfile.R
SRAdb/R/getFASTQinfo.R
SRAdb/R/getSRA.R
SRAdb/R/getSRAdbFile.R
SRAdb/R/getSRAfile.R
SRAdb/R/getSRAinfo.R
SRAdb/R/listSRAfile.R
SRAdb/R/sraConvert.R
SRAdb/R/sraGraph.R
SRAdb/R/startIGV.R
SRAdb/SRAdb-package.Rd
SRAdb/build
SRAdb/build/vignette.rds
SRAdb/inst
SRAdb/inst/CITATION
SRAdb/inst/doc
SRAdb/inst/doc/SRAdb.R
SRAdb/inst/doc/SRAdb.Rnw
SRAdb/inst/doc/SRAdb.pdf
SRAdb/inst/extdata
SRAdb/inst/extdata/SRR036007.chr1.hg18.bwa.sorted.bam
SRAdb/inst/extdata/SRR036007.chr1.hg18.bwa.sorted.bam.bai
SRAdb/inst/extdata/SRR036007.chr1.hg18.bwa.sorted.bam.tdf
SRAdb/inst/extdata/SRR036008.chr1.hg18.bwa.sorted.bam
SRAdb/inst/extdata/SRR036008.chr1.hg18.bwa.sorted.bam.bai
SRAdb/inst/extdata/SRR036008.chr1.hg18.bwa.sorted.bam.tdf
SRAdb/man
SRAdb/man/IGVclear.Rd
SRAdb/man/IGVcollapse.Rd
SRAdb/man/IGVgenome.Rd
SRAdb/man/IGVgoto.Rd
SRAdb/man/IGVload.Rd
SRAdb/man/IGVsession.Rd
SRAdb/man/IGVsnapshot.Rd
SRAdb/man/IGVsocket.Rd
SRAdb/man/IGVsort.Rd
SRAdb/man/SRAdb-package.Rd
SRAdb/man/ascpR.Rd
SRAdb/man/ascpSRA.Rd
SRAdb/man/colDescriptions.Rd
SRAdb/man/entityGraph.Rd
SRAdb/man/getFASTQfile.Rd
SRAdb/man/getFASTQinfo.Rd
SRAdb/man/getSRA.Rd
SRAdb/man/getSRAdbFile.Rd
SRAdb/man/getSRAfile.Rd
SRAdb/man/getSRAinfo.Rd
SRAdb/man/listSRAfile.Rd
SRAdb/man/sraConvert.Rd
SRAdb/man/sraGraph.Rd
SRAdb/man/startIGV.Rd
SRAdb/vignettes
SRAdb/vignettes/SRAdb.Rnw
SRAdb/vignettes/SRAdiagram.png
SRAdb/vignettes/sraGraph.png