Background: The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next\r\ngeneration of sequencing platforms including Illumina (Genome Analyzer, HiSeq, MiSeq, .etc), Roche 454 GS System,\r\nApplied Biosystems SOLiD System, Helicos Heliscope, PacBio RS, and others.\r\nResults: SRAdb is an attempt to make queries of the metadata associated with SRA submission, study, sample,\r\nexperiment and run more robust and precise, and make access to sequencing data in the SRA easier. We have parsed\r\nall the SRA metadata into a SQLite database that is routinely updated and can be easily distributed. The SRAdb\r\nR/Bioconductor package then utilizes this SQLite database for querying and accessing metadata. Full text search\r\nfunctionality makes querying metadata very flexible and powerful. Fastq files associated with query results can be\r\ndownloaded easily for local analysis. The package also includes an interface from R to a popular genome browser, the\r\nIntegrated Genomics Viewer.\r\nConclusions: SRAdb Bioconductor package provides a convenient and integrated framework to query and access\r\nSRA metadata quickly and powerfully from within R.
Loading....