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quast-software [2014/09/29 10:33]
aorth created
quast-software [2017/10/04 07:09]
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: 3.0
   * Added: September, 2014   * Added: September, 2014
-  * Link: http://bioinf.spbau.ru/en/quast+  * Updated: September, 2017 
 +  * Link: http://quast.sourceforge.net/quast
  
 ===== Usage ===== ===== 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/4.5 
 +$ quast.py --help</code>
  
 ===== Installation ====== ===== Installation ======
 Notes from the sysadmin during 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-4.5.tar.gz 
-tar xf quast-2.3.tar.gz +$ tar xf quast-4.5.tar.gz 
-sudo mkdir -p /export/apps/quast +$ cd quast-4.5 
-sudo cp -rv quast-2.3 /export/apps/quast/2.3 +sudo mkdir -p /export/apps/quast/4.5 
-sudo chown -R aorth:aorth /export/apps/quast/2.3 +sudo chown aorth /export/apps/quast/4.5 
-cd /export/apps/quast/2.+$ $ module load python/3.5.3 
-module load python/2.7.6 +$ python -m venv /export/apps/quast/4.5 
-./metaquast.py --test +$ . /export/apps/quast/4.5/bin/activate 
-cd libs/MUMmer3.23-linux +$ pip install -U setuptools pip 
-make +./setup.py install_full 
-cd ../.. +sudo chown -R root:root /export/apps/quast/4.5</code>
-./metaquast.py --test +
-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.txt · Last modified: 2020/04/07 08:27 by aorth