SRAdb: query and use public next-generation sequencing data from within R

BMC Bioinformatics

Software

Robert M Stephens¹  Paul S Meltzer²  Sean R Davis²  Yuelin Zhu³ 

[1] Advanced Biomedical Computing Center, National Cancer Institute-Frederick, SAIC-Frederick Inc., 21702, Frederick, MD, USA;Genetics Branch, National Cancer Institute, National Institutes of Health, 20892, Bethesda, MD, USA;Genetics Branch, National Cancer Institute, National Institutes of Health, 20892, Bethesda, MD, USA;Advanced Biomedical Computing Center, National Cancer Institute-Frederick, SAIC-Frederick Inc., 21702, Frederick, MD, USA;

关键词: Sequence Read Archive;    Fastq File;    Genomic Viewer;    Full Text Search;    Library Strategy;   

DOI  :  10.1186/1471-2105-14-19

 received in 2012-09-28, accepted in 2013-01-11,  发布年份 2013

来源: Springer

【 摘 要 】

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

【 授权许可】

Unknown   
© Zhu et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.