Ghana-Installation-software.md

@@ -552,7 +552,7 @@ Add this variable to the path :
             look at the scripts in /usr/local/bioinfo/abyss-2.1.5/bin
             tool + arguments
            
-# Repeatcout:
+# RepeatScout:
 
 Description: The purpose of the RepeatScout software is to identify repeat family
 sequences from genomes where hand-curated repeat databases (a la
@@ -567,7 +567,8 @@ URL: https://github.com/mmcco/RepeatScout
                      
             wget http://bix.ucsd.edu/repeatscout/RepeatScout-1.0.5.tar.gz
             tar xvfz RepeatScout-1.0.5.tar.gz -C /usr/local/bioinfo
-            cd /usr/local/bioinfo/RepeatScout-1.0.5
+            mv /usr/local/bioinfo/RepeatScout-1 /usr/local/RepeatScout-1.0.5
+            cd /usr/local/RepeatScout-1.0.5
             make
 
       
@@ -644,3 +645,35 @@ Add this variable to the path :
             tools + arguments
 
 
+# velvet:
+
+Description: http://www.ebi.ac.uk/~zerbino/velvet/
+
+URL: Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454
+
+
+
+### Installation:
+
+            wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
+            tar xvfz velvet_1.2.10.tar.gz -C /usr/local/bioinfo
+            mv /usr/local/bioinfo/velvet_1.2.10 /usr/local/velvet-1.2.10
+            cd /usr/local/velvet-1.2.10
+            make
+            chmod -R 755 /usr/local/bioinfo/velvet-1.2.10           
+            
+      
+
+Add this variable to the path :
+
+       echo  'export PATH=/usr/local/bioinfo/velvet-1.2.10:$PATH' >>/etc/profile
+       
+
+       source /etc/profile
+
+
+### Usage:
+            
+           velvetg + arguments
+           or velveth + arguments
+