SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing

• DOI: 10.1093/bioinformatics/bts337
• Publication Date: 2012-06-12T02:28:09Z
• Authors: Zhifu Sun; Saurabh Baheti; Sumit Middha; Rahul Kanwar; Yuji Zhang; Xing Li; Andreas S. Beutler; Eric Klee; Yan W. Asmann; E. Aubrey Thompson; Jean-Pierre A. Ko...
• Keywords: Bisulfite sequencing

Abstract Summary: Reduced representation bisulfite sequencing (RRBS) is a cost-effective approach for genome-wide methylation pattern profiling. Analyzing RRBS data challenging and specialized alignment/mapping programs are needed. Although such have been developed, comprehensive solution that provides researchers with good quality analyzable still lacking. To address this need, we developed Streamlined Analysis Annotation Pipeline (SAAP-RRBS) integrates read assessment/clean-up, alignment, extraction, annotation, reporting visualization. This package facilitates rapid transition from reads to fully annotated CpG report biological interpretation. Availability implementation: SAAP-RRBS freely available non-commercial users at the web site http://ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm. Contact: [e-mail] or [e-mail] Supplementary Information: Bioinformatics online.