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1. TrimGaloreTrimGalorePublic

   A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

   Perl 491 150

2. BismarkBismarkPublic

   A tool to map bisulfite converted sequence reads and determine cytosine methylation states

   HTML 414 105

3. SNPsplitSNPsplitPublic

   Allele-specific alignment sorting

   Perl 54 20

4. reStrainingOrderreStrainingOrderPublic

   A little QC tool that attempts to predict the genotype of mouse samples used, based on prior knowledge of high-quality SNPs from the Mouse Genomes Project

   LilyPond 5 1

5. IMPLICONIMPLICONPublic

   A processing guide for IMPLICON data (bisulfite amplicon data for imprinted loci)

   Python 2