DNPTrapper, a shotgun sequence finishing tool, designed to address the key sequence assembly problems caused by repeated regions in a genome. The program detects and visualizes single nucleotide differences between nearly identical repeat copies, and offers the overview and flexibility needed to rapidly resolve complex regions within a working session. The use of a database allows large amounts of data to be stored and handled, and allows viewing of mammalian size genomes. With DNPTrapper, it is possible to separate repeated regions that previously were considered impossible to resolve, and finishing tasks that previously took days or weeks can be resolved within hours or even minutes.
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BMC Bioinformatics, 2006 Mar 20; 7:155
DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions.
Arner, E, Tammi, MT, Tran, AN, Kindlund, E, Andersson B.