Parallel GENSENG

Parallel GENSENG is a parallel implementation of the GENSENG software for detecting copy number variations from high-throughput sequencing data.

This software runs exactly as the original code does, except that it utilizes multiple threads where possible. OpenMP was used for multi-threading so changes to the original code were minimal. For a demo, please download the sample data linked to below and follow the README from the tarball.

Example read count data:
http://www.cs.unc.edu/~wangwb09/GENSENG/reviseddata4hmm_300bpSlides_chr1.txt

Suggested transition matrix file
http://www.cs.unc.edu/~wangwb09/GENSENG/transition_init.dat

The original code can be found at these locations:
v0.1: http://www.cs.unc.edu/~wangwb09/GENSENG/GENSENG_download_page.html
v0.3: https://sourceforge.net/projects/genseng/

Features

detects CNVs from NGS data
utilizes HMM and negative binomial regression framework

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