QUAST (QUality ASsessment Tool) evaluates genome assemblies by computing various metrics.
See versions of quast which are available:
$ module avail quast
Load one version into your environment and run it:
$ module load quast/5.0.2 $ quast.py --help
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://downloads.sourceforge.net/project/quast/quast-5.0.2.tar.gz $ tar xf quast-5.0.2.tar.gz $ cd quast-5.0.2 $ sudo mkdir -p /export/apps/quast/5.0.2 $ sudo chown aorth /export/apps/quast/5.0.2 $ python3 -m venv /export/apps/quast/5.0.2 $ source /export/apps/quast/5.0.2/bin/activate $ pip install --upgrade pip setuptools $ pip install matplotlib $ ./setup.py install_full $ ./setup.py test $ sudo chown -R root:root /export/apps/quast/5.0.2
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