Next Generation Sequencing (NGS)/ABySS

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 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