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

• Version: 1.5.2
• Added: August, 2013
• Updated: March, 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/1.5.2/abyss-1.5.2.tar.gz
$ tar xf abyss-1.5.2.tar.gz 
$ cd abyss-1.5.2
$ scl enable devtoolset-2 bash
$ mkdir /tmp/abyss-build
$ cd /tmp/abyss-build
$ /tmp/abyss-1.5.2/configure --prefix=/export/apps/abyss/1.5.2 --with-boost=/export/apps/boost/1.50.0/include --with-mpi=/export/apps/openmpi/1.8.2
$ make -j4
$ sudo mkdir -p /export/apps/abyss/1.5.2
$ sudo chown aorth /export/apps/abyss/1.5.2
$ make install
$ sudo chown -R root:root /export/apps/abyss/1.5.2