Related Experiment Video
Updated: May 21, 2026
13:47
Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
Published on: February 24, 2015
SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing
Zhifu Sun1, Saurabh Baheti, Sumit Middha
1Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN 55905, USA. sun.zhifu@mayo.edu
Bioinformatics (Oxford, England)
|June 13, 2012
Summary
Analyzing reduced representation bisulfite sequencing (RRBS) data is now streamlined. Our new pipeline, SAAP-RRBS, simplifies the process from raw reads to annotated methylation reports for easier biological interpretation.
Area of Science:
- Genomics
- Epigenetics
- Bioinformatics
Background:
- Reduced representation bisulfite sequencing (RRBS) enables cost-effective genome-wide methylation profiling.
- Analysis of RRBS data requires specialized alignment tools, and a comprehensive solution is lacking.
Purpose of the Study:
- To develop a comprehensive pipeline for streamlined analysis and annotation of RRBS data.
- To facilitate the transition from sequencing reads to interpretable methylation reports.
Main Methods:
- Developed SAAP-RRBS, a pipeline integrating read quality assessment, clean-up, alignment, and methylation data extraction.
- Incorporated annotation, reporting, and visualization functionalities into the pipeline.
Main Results:
- SAAP-RRBS provides a comprehensive solution for RRBS data analysis.
- The pipeline generates fully annotated CpG methylation reports.
Conclusions:
- SAAP-RRBS significantly simplifies RRBS data analysis, enabling rapid biological interpretation.
- The freely available package supports non-commercial users.
