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SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing.
- Source :
-
Bioinformatics . Aug2012, Vol. 28 Issue 16, p2180-2181. 2p. - Publication Year :
- 2012
-
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. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 13674803
- Volume :
- 28
- Issue :
- 16
- Database :
- Academic Search Index
- Journal :
- Bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 78359939
- Full Text :
- https://doi.org/10.1093/bioinformatics/bts337