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grom-rd-software [2017/05/24 11:33] (current)
aorth created
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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>​
  
grom-rd-software.txt · Last modified: 2017/05/24 11:33 by aorth