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Background  Many genome projects are left unfinished due to complex, repeated regions. Finishing is the most time consuming step in sequencing and current finishing tools are not designed with particular attention to the repeat problem.    Results  We have developed DNPTrapper, a shotgun sequence finishing tool, specifically designed to address the problems posed by the presence of repeated regions in the target sequence. The program detects and visualizes single base 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. The program is available under an Open Source license.    Conclusion  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.

DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions