411 REFERENCE · Wikibooks
Next Generation Sequencing (NGS)/ABySS
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We need to get google sparsehash first assuming you don't have root privileges 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