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masurca-software [2014/09/30 12:05]
aorth
masurca-software [2018/11/10 18:38]
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: ​2.3.1+  * 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 ======
 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/​3.2.8/MaSuRCA-3.2.8.tar.gz 
-cd /​tmp/​MaSuRCA-2.3.1/​ +tar xf MaSuRCA-3.2.8.tar.gz 
-sudo mkdir -p /​export/​apps/​masurca/​2.3.1                                                                                                                                          ​ +sudo mkdir /​export/​apps/​masurca/​3.2.8 
-sudo chown aorth /​export/​apps/​masurca/​2.3.1 +sudo chown aorth /​export/​apps/​masurca/​3.2.
-DEST=/​export/​apps/​masurca/​2.3.1 ./​install.sh +$ sudo yum install perl-Env.noarch 
-sudo chown -R root:root /​export/​apps/​masurca/​2.3.1</​code>​ +DEST=/​export/​apps/​masurca/​3.2../​install.sh 
- +sudo chown -R root:root /​export/​apps/​masurca/​3.2.8</​code>​
-Get a download link for the tarball from: http://​www.genome.umd.edu/​masurca_form.html+
masurca-software.txt · Last modified: 2019/04/01 18:27 by aorth