Massively parallel DNA and RNA sequencing have become widely available, reducing the cost by several orders of magnitude and placing the capacity to generate gigabases to terabases of sequence data into the hands of individual investigators. These next-generation technologies have the potential to dramatically accelerate biological and biomedical research by enabling the comprehensive analysis of genomes and transcriptomes to become inexpensive, routine and widespread. The exploding volume of data has spurred the development of novel algorithmic approaches for primary analyses of sequence data in such areas as error correction, de novo genome assembly, novel transcript discovery, virus quasispecies assembly, etc. This workshop will bring together specialists to discuss the various mathematical and computational challenges presented by next-generation sequencing technologies.