Next Generation Sequencing (NGS)/ABySS

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We need to get google sparsehash first assuming you don't have root priviligies and your name is USER we install in a local include directory

 wget http://google-sparsehash.googlecode.com/files/sparsehash-1.11.tar.gz
 tar xvzf sparsehash-1.11.tar.gz
 cd sparsehash-1.11
 ./configure -prefix=/home/USER
 make
 make install


Now get ABySS (assuming you have the BOOST libraries installed)

 wget http://www.bcgsc.ca/downloads/abyss/abyss-1.2.7.tar.gz
 tar xzvf abyss-1.2.7.tar.gz
 cd abyss-1.2.7
 ./configure CPPFLAGS=-I/home/USER/include
 make

For more details about the installation process see the ABySS entry or install the .deb if you have a debian compliant system.

We now run ABySS with a kmer size of 25 and require at least n=10 links to join contigs.

 cd bin
 ./abyss-pe k=25 n=10 in='SRR001665_1.fastq SRR001665_2.fastq' name=ecoli