Significantly cheaper de novo sequencing technologies must be developed to fully understand the diversity of life. Although the technologies currently being developed focus on the easier problem of resequencing to study human variation, we are convinced that coupling them with significant advances in computational sequence assembly has the potential to dramatically reduce the cost of de novo (new species) sequencing as well.
Today's sequence assembly algorithms are based on certain assumptions of read length and base-error rate which do not hold for these new technologies. The paradigms of sequence assembly will shift dramatically in the face of the extremely high coverage of the new technologies, becoming more statistical in flavor. This project will develop the new classes of algorithms needed for tommorow's assemblers.
We have already developed a prototype assembler for new short-read sequencing technologies developed by Solexa, Helicos, and Applied Biosystems/Agencourt. These technologies achieve their cost efficiency by producing massive numbers of very short reads cheaply. We have demonstrated that extremely short reads suffice for assembly under certain conditions. This project asks you to help build a practical short-read fragment assembler for realistic error-models and levels of coverage.
Financial support is potentially available for this project, and room for one or two students.