Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler.

• Version: 2.0.2
• Added: August, 2013
• Updated: October, 2017
• K-mer size: 64 (default at compile time)
• Link: http://www.bcgsc.ca/platform/bioinfo/software/abyss

See versions of abyss which are available:

$ module avail abyss

Load one version into your environment and run it:

$ module load abyss/2.0.2
$ abyss-pe --help

Notes from the sysadmin during installation:

$ cd /tmp
$ wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.0.2/abyss-2.0.2.tar.gz
$ tar xf abyss-2.0.2.tar.gz 
$ cd abyss-2.0.2
$ scl enable devtoolset-4 bash
$ ./configure --prefix=/export/apps/abyss/2.0.2 --with-boost=/export/apps/boost/1.65.1/include --with-mpi=/export/apps/openmpi/1.8.2
$ make -j4
$ sudo mkdir /export/apps/abyss/2.0.2
$ sudo chown aorth /export/apps/abyss/2.0.2
$ make install
$ sudo chown -R root:root /export/apps/abyss/2.0.2