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quast-software [2015/06/09 16:36]
aorth
quast-software [2020/04/07 08:27] (current)
aorth
Line 1: Line 1:
 ====== quast ====== ====== quast ======
 +QUAST (QUality ASsessment Tool) evaluates genome assemblies by computing various metrics.
  
 ===== Information ===== ===== Information =====
  
-  * Version: 2.3+  * Latest Version: 5.0.2
   * Added: September, 2014   * Added: September, 2014
-  * Link: http://bioinf.spbau.ru/en/quast+  * Updated: April, 2020 
 +  * Link: http://quast.sourceforge.net/quast
  
 ===== Usage ===== ===== Usage =====
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 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 ====== ===== Installation ======
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 <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.
-cd /export/apps/quast/2.3 +python3 -m venv /export/apps/quast/5.0.
-$ 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>
quast-software.1433867777.txt.gz · Last modified: 2015/06/09 16:36 by aorth