Management and visualization of whole genome shotgun assemblies using SAM

We have designed and implemented a system to manage whole genome shotgun sequences and whole genome sequence assembly dataflow. The Sequence Assembly Manager (SAM) consists primarily of a MySQL relational database and Perl applications designed to easily manipulate and coordinate the analysis of sequence information and to view and report genome assembly progress through its Common Gateway Interface (CGI) web interface. The application includes a tool to compare sequence assemblies to fingerprint maps that has been used successfully to improve and validate both maps and sequence assemblies of the sp. RHA1 and neoformans WM276 genomes.