Wikibooks

Next Generation Sequencing (NGS)/ABySS

< Next Generation Sequencing (NGS)
This page may need to be reviewed for quality.

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
Retrieved from "https://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS)/ABySS"