bspipe

BSpipe is a comprehensive pipeline from sequence quality control and mapping to functional analysis of differentially methylated regions:
(1) sequencing quality assessment,
(2) sequence cleaning,
(3) sequence read mapping,
(4) methylation quantification,
(4) sample comparisons based on methylation profile,
(5) identification of DMRs (differentially methylated regions),
(6) annotation of DMRs,
(7) functional analysis of differentially methylated genes,
(8) generation of input files for visualization, and
(9) support for advanced sequencing technologies such as TAB-seq, OxBS-seq, MAP-it, and NOMe-seq.