Monday, 11 October 2010

Installing SOLiD™ System de novo Accessory Tools 2.0 with Velvet and MUMmer

howto install on CentOS 5.4 

 wget #just to keep a record
 tar zxvf denovo2.tgz
 cp velvet_0.7.55.tgz denovo2 #you can use mv if you don’t mind downloading again
 cp MUMmer3.22.tar.gz denovo2
 cd denovo2
 tar zxvf velvet_0.7.55.tgz
 tar zxvf MUMmer3.22.tar.gz
 cd MUMmer3.22/src/kurtz #this was the part where I deviated from instructions
 gmake mummer #Might be redundant but running gmake at root dir gave no binary
 gmake |tee gmake-install.log
Next step:
download the example data to run through the pipeline

This is a 50X50 Mate pair library from DH10B produced by SOLiD™ system.The set includes .csfasta and .qual files for F3 and R3. The insert size of the library is 1300bp and it is about 600X coverage of the DH10B genome. The results from MP library in the de novo documents are generated from this dataset.


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