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

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. Kocher

Research output: Contribution to journalArticle

33 Scopus citations

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.

Original languageEnglish (US)
Article numberbts337
Pages (from-to)2180-2181
Number of pages2
JournalBioinformatics
Volume28
Issue number16
DOIs
StatePublished - Aug 2012

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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