QUAST (QUality ASsessment Tool) evaluates genome assemblies by computing various metrics.

• Latest Version: 4.5
• Added: September, 2014
• Updated: January, 2019
• Link: http://quast.sourceforge.net/quast

See versions of quast which are available:

$ module avail quast

Load one version into your environment and run it:

$ module load quast/4.5
$ quast.py --help

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://downloads.sourceforge.net/project/quast/quast-4.5.tar.gz
$ tar xf quast-4.5.tar.gz
$ cd quast-4.5
$ sudo mkdir -p /export/apps/quast/4.5
$ sudo chown aorth /export/apps/quast/4.5
$ module load python/3.5
$ python -m venv /export/apps/quast/4.5
$ . /export/apps/quast/4.5/bin/activate
$ pip install --upgrade setuptools pip
$ pip install matplotlib
$ ./setup.py install_full
$ sudo chown -R root:root /export/apps/quast/4.5

You can test the installation using the test data from the source tarball:

$ quast.py test_data/contigs_1.fasta test_data/contigs_2.fasta -R test_data/reference.fasta.gz -G test_data/genes.gff