Enabling personal genomics: discovering and understanding genetic variation

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High-throughput sequencing (HTS) technologies, such as Illumina/Solexa and AB SOLiD, are able to sequence a full human genome per week at a cost 200-fold less than previous methods. The resulting data consist of pieces - reads - about 35-120 nucleotides long, from unknown locations in the genome. Analysis of these datasets poses an unprecedented informatics challenge, both because of the sheer number of reads that a single run of an HTS machine can produce, and because the reads are significantly shorter than previously available. Methods for the analysis of short-read datasets have started to become available over the last few years, and while some of the problems are close to being solved with reliable tools freely available to the scientific community, there are still many challenges remaining. Under this proposal I plan to develop methodologies to analyze HTS data in order to discover and understand genomic variants, and to apply these methods towards the study of the Ciona savignyi model organism.