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--- masurca-software [2014/06/11 13:05] – created aorth
+++ masurca-software [2019/04/01 15:27] – aorth
@@ Line 1: / Line 1: @@
 ====== 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 =====
-  * Version: 2.2.1
+  * Version: 3.3.1
-  * Added: June, 2014
+  * Added: September, 2014
-  * Link: http://www.genome.umd.edu/masurca.html
+  * Updated: April, 2019
+  * Link: https://github.com/alekseyzimin/masurca
 ===== 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 ======
 Notes from the sysadmin during installation:
-<code>wget ftp://ftp.genome.umd.edu/pub/MaSuRCA/v2.2.1/MaSuRCA-2.2.1.tar.gz
+<code>$ cd /tmp
-tar zxf MaSuRCA-2.2.1.tar.gz  -C /tmp/
+$ wget https://github.com/alekseyzimin/masurca/releases/download/v3.3.1/MaSuRCA-3.3.1.tar.gz
-cd /tmp/MaSuRCA-2.2.1/
+$ tar xf MaSuRCA-3.3.1.tar.gz
-sudo mkdir -p /export/apps/masurca/2.2.1
+$ cd MaSuRCA-3.3.1
-sudo chown aorth /export/apps/masurca/2.2.1
+$ sudo mkdir /export/apps/masurca/3.3.1
-scl enable devtoolset-1.1 bash
+$ sudo chown aorth /export/apps/masurca/3.3.1
-DEST=/export/apps/masurca/2.2.1 ./install.sh
+$ sudo yum install perl-Env.noarch
-sudo chown -R root:root /export/apps/masurca/2.2.1</code>
+$ DEST=/export/apps/masurca/3.3.1 ./install.sh
+$ sudo chown -R root:root /export/apps/masurca/3.3.1</code>