New sequencing methods generate data that can allow the assembly of microbial genome sequences in days. With such revolutionary advances in technology come new challenges in methodologies and informatics. In this article, we review the capabilities of high-throughput sequencing technologies and discuss the many options for getting useful information from the data. New sequencing technologies, such as Solexa, 454 pyrosequencing and SOLiD, developed by Illumina, Roche and Applied Biosystems, respectively, are set to revolutionize microbiology by dramatically increasing throughput and reducing costs of DNA sequencing. Applications include de novo genome sequence assembly, metagenomics, sRNA discovery, detection of polymorphisms, expression profiling and epigenetics. As well as sequence alignment and assembly, there is a need for downstream processing of data into a form that is accessible to biologists. Many freely available software packages are available for dealing with the large datasets generated by these applications.