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A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Assembly Based ReAligner

A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clustering: alignWigToBed; )

A Java package for non-invasive cancer diagnosis using methylation profiles of cell-Free DNA.