ILRI Research Computing

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

===== Information =====

  * Latest Version: 5.0.2
  * Added: September, 2014
  * Updated: April, 2020
  * Link: http://quast.sourceforge.net/quast

===== Usage =====

See versions of quast which are available:
<code>$ module avail quast</code>

Load one version into your environment and run it:
<code>$ module load quast/5.0.2
$ quast.py --help</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ 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</code>

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

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