Friday, July 6, 2012

Fwd: SRMA: an R package for resequencing array data analysis

Fwd: please follow footer link
SRMA: an R package for resequencing array data analysis:

Summary: Sequencing by hybridization to oligonucleotides has evolved into an inexpensive, reliable and fast technology for targeted sequencing. Hundreds of human genes can now be sequenced within a day using a single hybridization to a resequencing microarray. However, several issues inherent to these arrays (e.g. cross-hybridization, variable probe/target affinity) cause sequencing errors and have prevented more widespread applications. We developed an R package for resequencing microarray data analysis that integrates a novel statistical algorithm, sequence robust multi-array analysis (SRMA), for rare variant detection with high sensitivity (false negative rate, FNR 5%) and accuracy (false positive rate, FPR 1x10–5). The SRMA package consists of five modules for quality control, data normalization, single array analysis, multi-array analysis and output analysis. The entire workflow is efficient and identifies rare DNA single nucleotide variations and structural changes such as gene deletions with high accuracy and sensitivity.

Availability:http://cran.r-project.org/, http://odin.mdacc.tmc.edu/~wwang7/SRMAIndex.html

Contact:wwang7@mdanderson.org

Supplementary information:Supplementary data are available at Bioinformatics online.



(Original Post: Bioinformatics - current issue.)