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--- quast-software [2014/09/29 10:33] – created aorth
+++ quast-software [2020/04/07 08:27] (current) – aorth
@@ Line 1: / Line 1: @@
 ====== quast ======
+QUAST (QUality ASsessment Tool) evaluates genome assemblies by computing various metrics.
 ===== Information =====
-  * Version: 2.3
+  * Latest Version: 5.0.2
   * Added: September, 2014
-  * Link: http://bioinf.spbau.ru/en/quast
+  * Updated: April, 2020
+  * Link: http://quast.sourceforge.net/quast
 ===== Usage =====
-=== See versions of quast which are available ===
+See versions of quast which are available:
-<code>module avail quast</code>
+<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
+<code>$ cd /tmp
-wget 'http://downloads.sourceforge.net/project/quast/quast-2.3.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fquast%2Ffiles%2F&ts=1411971659&use_mirror=tenet' -O quast-2.3.tar.gz
+$ wget https://downloads.sourceforge.net/project/quast/quast-5.0.2.tar.gz
-tar xf quast-2.3.tar.gz
+$ tar xf quast-5.0.2.tar.gz
-sudo mkdir -p /export/apps/quast
+$ cd quast-5.0.2
-sudo cp -rv quast-2.3 /export/apps/quast/2.3
+$ sudo mkdir -p /export/apps/quast/5.0.2
-sudo chown -R aorth:aorth /export/apps/quast/2.3
+$ sudo chown aorth /export/apps/quast/5.0.2
-cd /export/apps/quast/2.3
+$ python3 -m venv /export/apps/quast/5.0.2
-module load python/2.7.6
+$ source /export/apps/quast/5.0.2/bin/activate
-./metaquast.py --test
+$ pip install --upgrade pip setuptools
-cd libs/MUMmer3.23-linux
+$ pip install matplotlib
-make
+$ ./setup.py install_full
-cd ../..
+$ ./setup.py test
-./metaquast.py --test
+$ sudo chown -R root:root /export/apps/quast/5.0.2</code>
-sudo chown -R root:root /export/apps/quast/2.3</code>
-===== Running =====
+You can test the installation using the test data from the source tarball:
-After loading the module, consult the built-in help:
-<code>metaquast.py  --help</code>
+<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>