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masurca-software [2014/09/30 09:05]
aorth
masurca-software [2019/04/01 15:27]
aorth
Line 1: Line 1:
 ====== 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: 2.3.1+  * Version: 3.3.1
   * Added: September, 2014   * Added: September, 2014
-  * Link: http://www.genome.umd.edu/masurca.html+  * Updated: April, 2019 
 +  * 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/3.3.1 
 +masurca</code>
  
 ===== Installation ====== ===== Installation ======
 Notes from the sysadmin during installation: Notes from the sysadmin during installation:
  
-<code>wget 'http://www.genome.umd.edu/download_masurca.php?a=YS5vcnRoQGNnaWFyLm9yZw&b=src&c=36046372&d=3b9bd77c404ec8a48b1fe42aac9a3eb6082f8e58' -O MaSuRCA-2.3.1.tar.gz +<code>$ cd /tmp 
-tar zxf MaSuRCA-2.3.1.tar.gz -C /tmp/ +wget https://github.com/alekseyzimin/masurca/releases/download/v3.3.1/MaSuRCA-3.3.1.tar.gz 
-cd /tmp/MaSuRCA-2.3.1/ +tar xf MaSuRCA-3.3.1.tar.gz 
-sudo mkdir -p /export/apps/masurca/2.3.1                                                                                                                                           +cd MaSuRCA-3.3.1 
-sudo chown aorth /export/apps/masurca/2.3.1 +sudo mkdir /export/apps/masurca/3.3.1 
-DEST=/export/apps/masurca/2.3.1 ./install.sh +sudo chown aorth /export/apps/masurca/3.3.1 
-sudo chown -R root:root /export/apps/masurca/2.3.1</code> +$ sudo yum install perl-Env.noarch 
- +DEST=/export/apps/masurca/3.3.1 ./install.sh 
-Get a download link for the tarball from: http://www.genome.umd.edu/masurca_form.html+sudo chown -R root:root /export/apps/masurca/3.3.1</code>
masurca-software.txt · Last modified: 2019/04/01 15:27 by aorth