AByss/Trans-AByss on Helix
AByss is a de novo, parallel, paired-end sequence assembler. Trans-ABySS is a software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.
The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.
$ module avail abyss -------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles --------------------------------------------------------
abyss/1.3.1 abyss/1.3.2 abyss/1.3.4 abyss/1.3.5(default) $ module load abyss $ module list Currently Loaded Modulefiles: 1) abyss/1.3.5
$ module unload abyss $ module load abyss/1.3.2 $ module show abyss ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/abyss/1.3.5: module-whatis Sets up abyss 1.3.5 prepend-path PATH /usr/local/apps/abyss/1.3.5/bin prepend-path PATH /usr/local/transabyss/bin prepend-path PATH /usr/local/OpenMPI/1.6/gnu/eth/bin -------------------------------------------------------------------
How To Use
Abyss Example
helix $ module load abyss helix $ `which abyss-pe` k=25 n=10 in='input1 input2' name=FileName
Trans-Abyss Example
helix $ module load transabyss helix $ python trans-abyss.py -<stage> -n <input file>
Documentation
http://www.bcgsc.ca/platform/bioinfo/software/abyss
http://www.bcgsc.ca/downloads/trans-abyss/data/trans-abyss-manual-v1.4.4.pdf
