Software Packages

Department of Quantitative Health Sciences
Mayo Clinic Research
Formerly known as the Department of Health Sciences Research

Related links: Division Overview R Shiny Applications


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. With this package, bioinformaticians or investigators can start from sequencing reads and get a fully annotated CpG methylation report quickly allowing more time for biological interpretation. The SAAP-RRBS program:

  • Conducts read quality check, adapter trimming, alignment, methylation extraction, annotation and visualization for sequence reads in a fastq format (single or pair end RRBS).
  • Conducts further downstream analyses for aligned BAM files from other RRBS aligners (single end RRBS).
  • Conducts comprehensive annotations for a CpG list with chromosome and location.
  • Is highly automatic and fast. To run the whole pipeline for a RRBS sample with 50 million of reads takes 4-6 hours.
  • Offers two modes of run. For users without a cluster environment, it can be run in a single Linux machine, one sample at time (non-sge mode).
  • Allows users with a cluster environment to submit jobs to the cluster to run multiple samples simultaneously for fast processing (sge mode).
  • Can handle both single end and pair end sequencing.
  • Provides summary reports for all samples in a run so users can quickly grasp their data.
  • Adapts for a different aligner and is extensible to the whole genome sequencing data.

Authors: Zhifu Sun, Saurabh Baheti, Sumit Middha, Rahul Kanwar, Y. Zhang, X. Li, Andreas S. Beutler, Eric W. Klee, Yan W. Asmann, E. Aubrey Thompson, Jean-Pierre A. Kocher

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

Saurabh Baheti

Zhifu Sun, M.D.

Page last modified: October 24, 2014