Overview
The Sequence Assembly project is being led by Dr. Corbin Jones, an assistant professor in the Department of Biology at UNC. UNC as well as other research institutes are beginning to take advantage of next generation genetic sequencing technologies which allow for relatively inexpensive and rapid determination of genetic sequences. This technology has a multitude of uses in genetic analysis and biological research and is poised to enable significant discoveries. One difficulty is that these newer sequencing technologies are only able to sequence DNA into short segments, which then must be assembled into complete sequences using computer software. Dr. Jones, working with others in his lab, have developed a new computer algorithm termed VCAKE which performs this assembly process. However, the algorithm is very computer intensive and running it on modest sized genomes takes many hours. RENCI is working with Dr. Jones to produce a subsequent version of the program that has much improved run-time performance and incorporates automatic setting of some of the difficult to set parameters. This program is being make available to the broader community and will assist in allowing research groups to effectively leverage these new sequencing technologies.
RENCI Collaboration
RENCI experts are working to develop more efficient implementations of the VCAKE algorithm to increase it’s performance.
Funding
State Funded
Collaborators
- Corbin Jones, assistant professor, Department of Biology, UNC-Chapel Hill
- Josie Reinhardt, graduate student, Department of Biology, UNC-Chapel Hill
Project Team
- Nassib Nassar
- Dave Bowman
- Xiaojun Guan
- Charles Schmitt
