General Information
| Description | Streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing |
| Homepage | http://ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm |
Publications
SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing
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.edu
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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