Methylation Integration (Mint) Pipeline

Github site:

The mint pipeline analyzes single-end reads coming from sequencing assays measuring DNA methylation and hydroxymethylation. The pipeline analyzes reads from both bisulfite-converted assays such as WGBS and RRBS, and from pulldown assays such as MeDIP-seq, hMeDIP-seq, and hMeSeal. Moreover, with data measuring both 5-methylcytosine (5mc) and 5-hydroxymethylcytosine (5hmc), the mint pipeline integrates the two data types to classify genomic regions of 5mc, 5hmc, a mixture, or neither.
The pipeline is available as both a command line( and a Galaxy graphical user interface too( Both implementations require minimal configuration while remaining flexible to experiment specific needs.