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


METHODS
SAAP-RRBS is freely available to non-commercial users at the web site http://ndc.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm.
Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN 55905, USA. sun.zhifu@mayo.edu
Zhifu
Z
Sun
Saurabh
S
Baheti
Sumit
S
Middha
Rahul
R
Kanwar
Yuji
Y
Zhang
Xing
X
Li
Andreas S
AS
Beutler
Eric
E
Klee
Yan W
YW
Asmann
E Aubrey
EA
Thompson
Jean-Pierre A
JP
Kocher
D019295:Computational Biology / Q000379:methods; D018899:CpG Islands; D019175:DNA Methylation; D023281:Genomics; D058977:Molecular Sequence Annotation / Q000379:methods*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013447:Sulfites
D013447:Sulfites; C042345:hydrogen sulfite