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

• Version: 2.1.4
• Added: August, 2013
• Updated: November, 2018
• K-mer size: 128 (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/2.1.4
$ abyss-pe help

Notes from the sysadmin during installation:

$ cd /tmp
$ wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.1.4/abyss-2.1.4.tar.gz
$ tar xf abyss-2.1.4.tar.gz
$ cd abyss-2.1.4
$ sudo yum install sparsehash-devel.x86_64 openmpi-devel.x86_64
$ ./configure --prefix=/export/apps/abyss/2.1.4
$ make -j4
$ sudo mkdir -p /export/apps/abyss/2.1.4
$ sudo chown aorth /export/apps/abyss/2.1.4
$ make install
$ sudo chown -R root:root /export/apps/abyss/2.1.4