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

Zhifu D Sun, Saurabh Baheti, Sumit Middha, Rahul Kanwar, Yuji Zhang, Xing Li, Andreas S Beutler, Eric W Klee, Yan Asmann, E Aubrey Thompson, Jean-Pierre Kocher

Research output: Contribution to journalArticle

31 Citations (Scopus)

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

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Methylation
Sequencing
Annotation
Data analysis
Pipelines
Alignment
Visualization
Genes
Research Personnel
Genome
Quality Assessment
Costs and Cost Analysis
Profiling
Integrate
hydrogen sulfite
Data Curation
Costs

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

SAAP-RRBS : Streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. / Sun, Zhifu D; Baheti, Saurabh; Middha, Sumit; Kanwar, Rahul; Zhang, Yuji; Li, Xing; Beutler, Andreas S; Klee, Eric W; Asmann, Yan; Thompson, E Aubrey; Kocher, Jean-Pierre.

In: Bioinformatics, Vol. 28, No. 16, bts337, 08.2012, p. 2180-2181.

Research output: Contribution to journalArticle

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