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

• Version: 1.9.0
• Added: August, 2013
• Updated: June, 2015
• 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

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/bcgsc/abyss/releases/download/1.9.0/abyss-1.9.0.tar.gz
$ tar -xvf abyss-1.9.0.tar.gz
$ cd abyss-1.9.0
$ scl enable devtoolset-2 bash
$ sudo mkdir /export/apps/abyss/1.9.0
$ sudo chown joguya:joguya /export/apps/abyss/1.9.0
$ CC=clang ./configure --prefix=/export/apps/abyss/1.9.0 --with-boost=/export/apps/boost/1.50.0/include --with-mpi=/export/apps/openmpi/1.8.2
$ make -j4
$ make install
$ sudo chown -R root:root /export/apps/abyss/1.9.0