A tool to generate high-quality methylation maps

Guillermo Barturen, Antonio Rueda, Josť L. Oliver and Michael Hackenberg

Software Download

Examples Download

For questions, feedback, etc please contact to: Michael Hackenberg (,


  • Version 1.4: 28/02/2014
  • Improved adapter removal

    Pair-End non-directional aligment included

    Direct SAM output

    LOG output extended

  • Version 1.2: 04/12/2012
  • from SAMtools package has been included on the Pipeline.

    CreateSequenceDictionary.jar from PicardTools has been included on the Pipeline. has been deleted from the package.

    We recommend to extract Methylation levels and SNVs with MethylExtract (

  • Version 1.1: 02/09/2011
  • Pair-end alignments processing has been implemented.

    Bowtie parameters for pair-end reads (I and X) have been implemented.

    "solexa1.3-quals" quality option has been implemented.

    NGSmethPipe will try now to align reads with shorter length than the seed.

    "nomaqround", "tryhard" and "chunkmbs" Bowtie parameters for single-end and pair-end reads have been now implemented.

    Now Bowtie will not be run in quite mode.

    Bug corrected: when no reads are aligned, the percentage of aligned reads can be 0.

    Bug corrected: reads IDs can have backslash (/).

  • Version 1.0: 01/07/2011
  • All basic functions working.

© Computational Genomics and Bioinformatics Group
Dept. of Genetics & Inst. of Biotechnology
University of Granada, Spain