This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We will be examining the use of novel algorithms to reassemble short sequence reads from the newest generation of genome sequencing machines. The technique of reassembling the short reads employs much higher coverage of the genome than earlier techniques. We believe that the best approach to this problem is to use a very large (>1 TB) shared memory machines to hold all of the short reads in main memory during the reassembly process. Accessing disk to connect the reads will make the technique unacceptably slow. The technique we expect to employ will use the work presented by Daniel R. Zerbino and Ewan Birney in """"""""Velvet: Algorithms for de novo short read assembly using de Bruijn graphs"""""""" published in 2008 18: 821-829 Genome Research. If our initial study proves the concept then the next phase of the work will be to parallelize the algorithm as its current implementation is serial. This study will allow us to determine if investing in a serial implementation is likely to be rewarding.
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