Project Leaders:
Inanc Birol, Steven Jones

Lead Institution:       
Canada’s Michael Smith Genome Sciences Centre

Research Funding Program:
SOF 2

 Scientists will develop bio-informatic tools enabling more accurate and cost-effective DNA sequencing.  Short read sequencing technologies profoundly altered the field of genomics, bringing down the cost of sequencing projects, and providing researchers unprecedented volumes of data. The BC Genome Sciences Centre (GSC) is an early access site for one of the short sequencing technologies and it has put the province on the forefront of this revolution.

Although genome sciences research projects using the new technology mostly take advantage of previously sequenced genomes to conduct comparative genomics studies, several teams have also developed tools for the assembly of de novo sequencing using next generation sequencing technologies. Such tools have not only enabled de novo sequencing studies, but also found application in comparative genomics as well by offering a complementary approach to alignment-based analysis methods. Until the GSC developed a parallel assembly tool called ABySS, however, these were limited to assembling megabase-scale genomes, hence, excluding investigations with the human genome.

Despite their success and utility, short read de novo assembly tools build draft assemblies of the studied genomes, and they need to be followed up by traditional and expensive sequence finishing experiments. With this project, researchers will develop ABySS into a short sequence assembly and finishing tool that alters this paradigm. Instead of designing primers and/or building reduced representation libraries, this new paradigm will make use of paired-end sequencing technology and experiments with various insert sizes in an iterative manner to finish genomes.

The ABySS assembly tool has already generated international interest, and with added sequence finishing capabilities, it will maintain the position of British Columbia at the cutting edge of genome sciences.

Related Links:
Funding Awarded > SOF 2