High-throughput sequencing (HTS) technologies are revolutionizing the way biologists acquire and analyze genomic data. HTS instruments, such as the Illumina Genomic Analyzer and the Applied Biosystems SOLiD System, are currently able to sequence tens of gigabases per week, at a cost of 200-fold less than previous methods, potentially enabling the routine sequencing of human and other genomes. Over the last few years the promise of HTS technologies has become a reality, however, realizing that the full promise of these technologies requires the development of computational methods that can analyze the resulting datasets to infer biological meaning. HTS can be used to study many biological problems, including assembling genomes of new organisms, identifying genome variation within a population, discovering novel transcripts, analyzing gene expression, discerning the regulatory mechanisms behind the expression levels and profiling the metagenome of a community. While many HTS datasets are readily available, the main bottleneck in the analysis is the dearth of computational methods that are able to directly answer biologists questions from these datasets.