ILRI Research Computing

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====== GROM-RD ======
Analyzes multiple biases in read coverage to detect CNVs in NGS data. To overcome a typical weakness of read depth (RD) methods, GROM-RD employs a CNV search using size-varying overlapping windows to improve breakpoint resolution. GROM-RD was able to improve RD sensitivity, specificity, and breakpoint accuracy compared to CNVnator and RDXplorer, the two most frequently used RD algorithms. Additionally, GROM-RD had a short run time that was relatively insensitive to read coverage indicating excellent scalability of the method for different datasets.

===== Information =====

  * Version: 1.0
  * Added: May, 2017
  * Link: http://grigoriev.rutgers.edu/software/grom-rd/index.html

===== Usage =====

See which versions of grom-rd are available:
<code>$ module avail grom-rd</code>

Load groovy
<code>$ module load grom-rd/1.0</code>

===== Installation ======

Notes from the sysadmin during installation:

<code>$ cd /tmp
$ wget http://grigoriev.rutgers.edu/software/grom-rd/GROM-RD_v1.0.tar.gz
$ tar xf GROM-RD_v1.0.tar.gz
$ cd GROM-RD_v1.0
$ make
$ sudo mkdir -p /export/apps/grom-rd/1.0
$ sudo cp bin/GROM-RD  /export/apps/grom-rd/1.0</code>