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 openmpi3-devel.x86_64
$ export CPPFLAGS='-pthread -I/usr/include/openmpi3-x86_64'
$ export LIBS='-Wl,-rpath -Wl,/usr/lib64/openmpi3/lib -Wl,--enable-new-dtags -L/usr/lib64/openmpi3/lib -lmpi'
$ ./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
$ sudo yum remove sparsehash-devel.x86_64 openmpi3-devel.x86_64

There is currently a bug in configure's ability to detect the system's OpenMPI so we have to set the environment variables manually before building.