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quast

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

Information

Usage

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

Installation

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
quast-software.txt · Last modified: 2020/04/07 11:27 by aorth