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masurca-software [2014/11/02 13:30]
aorth
masurca-software [2018/11/10 18:38] (current)
aorth [Usage]
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 ====== MaSuRCA ====== ====== MaSuRCA ======
-MaSuRCA ​is whole genome assembly software. It combines the efficiency ​of the de Bruijn ​graph and Overlap-Layout-Consensus ​(OLC) approaches. ​MaSuRCA can assemble data sets containing only short reads from Illumina ​sequencing or a mixture of short reads and long reads (Sanger, 454).+The MaSuRCA ​(Maryland Super Read Cabog Assembler) assembler ​combines the benefits ​of deBruijn ​graph and Overlap-Layout-Consensus ​assembly ​approaches. ​Since version 3.2.1 it supports hybrid assembly with short Illumina reads and long high error PacBio/​MinION data.
  
 ===== Information ===== ===== Information =====
  
-  * Version: ​2.3.2+  * Version: 3.2.8
   * Added: September, 2014   * Added: September, 2014
-  * Link: http://www.genome.umd.edu/masurca.html+  ​* Updated: November, 2018 
 +  ​* Link: https://github.com/​alekseyzimin/masurca
  
 ===== Usage ===== ===== Usage =====
 +See versions of masurca which are available:
  
-=== See versions of masurca ​which are available === +<​code>​$ module avail masurca</​code>​ 
-<​code>​module ​avail masurca</​code>​+ 
 +Load one version into your environment and run it: 
 +<​code>​module ​load masurca/​3.2.8 
 +masurca</​code>​
  
 ===== Installation ====== ===== Installation ======
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 <​code>​$ cd /tmp <​code>​$ cd /tmp
-$ wget 'http://www.genome.umd.edu/download_masurca.php?​a=YS5vcnRoQGNnaWFyLm9yZw&​b=src&​c=38900637&​d=47784a9fd97c4cc396300a9c11cc9ab3096b11c3'​ -O MaSuRCA-2.3.2.tar.gz +$ wget https://github.com/​alekseyzimin/​masurca/​releases/​download/​3.2.8/​MaSuRCA-3.2.8.tar.gz 
-$ tar xf MaSuRCA-2.3.2.tar.gz  +$ tar xf MaSuRCA-3.2.8.tar.gz 
-cd MaSuRCA-2.3.2 +sudo mkdir /​export/​apps/​masurca/​3.2.8 
-mkdir -p /​export/​apps/​masurca/​2.3.2 +$ sudo chown aorth /​export/​apps/​masurca/​3.2.8 
-$ sudo chown aorth /​export/​apps/​masurca/​2.3.2 +sudo yum install perl-Env.noarch 
-scl enable devtoolset-2 bash +$ DEST=/​export/​apps/​masurca/​3.2.8 ./​install.sh 
-$ DEST=/​export/​apps/​masurca/​2.3.2 ./​install.sh +$ sudo chown -R root:root /​export/​apps/​masurca/​3.2.8</​code>​
-$ sudo chown -R root:root /​export/​apps/​masurca/​2.3.2</​code>​ +
- +
-Get a download link for the tarball from: http://​www.genome.umd.edu/​masurca_form.html+
masurca-software.1414924214.txt.gz · Last modified: 2014/11/02 13:30 by aorth