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Over the last few years there has been a revolution in DNA sequencing technology that has brought down the cost of DNA sequencing and made the sequencing of an increasing number of genomes both feasible and cost effective. There has also been a dramatic shift in the type of sequence data being generated, with vast numbers of short reads or pairs of short reads replacing the traditional relatively long reads produced by Sanger sequencing. These changes in data quantity and format have led to a rethinking of sequence data management, storage, and visualization, and provide a challenge for bioinformatics. The vast amount of sequence data that will will be generated over the next few years will require a change in what data are stored and how users query the information.