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- Title
SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.
- Authors
Sun, Zhifu; Baheti, Saurabh; Middha, Sumit; Kanwar, Rahul; Zhang, Yuji; Li, Xing; Beutler, Andreas S.; Klee, Eric; Asmann, Yan W.; Thompson, E. Aubrey; Kocher, Jean-Pierre A.
- Abstract
Summary: Reduced representation bisulfite sequencing (RRBS) is a cost-effective approach for genome-wide methylation pattern profiling. Analyzing RRBS sequencing data is challenging and specialized alignment/mapping programs are needed. Although such programs have been developed, a comprehensive solution that provides researchers with good quality and analyzable data is still lacking. To address this need, we have developed a Streamlined Analysis and Annotation Pipeline for RRBS data (SAAP-RRBS) that integrates read quality assessment/clean-up, alignment, methylation data extraction, annotation, reporting and visualization. This package facilitates a rapid transition from sequencing reads to a fully annotated CpG methylation report to biological interpretation.Availability and implementation: SAAP-RRBS is freely available to non-commercial users at the web site http://ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm.Contact: baheti.saurabh@mayo.edu or sun.zhifu@mayo.eduSupplementary Information: Supplementary data are available at Bioinformatics online.
- Subjects
PIPELINES; SULFITES; METHYLATION; COST effectiveness; DATA extraction; BIOINFORMATICS
- Publication
Bioinformatics, 2012, Vol 28, Issue 16, p2180
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/bts337