Finishing Repetitive Regions Automatically with Dupfinisher

Currently, the genome sequencing community is producing shotgun sequence data at a very high rate, but genome finishing is not keeping pace, even with the help from several automated finishing tools, such as autoFinish. One reason for the slow progress in finishing is that repetitive regions longer than the length of a sequencing read cannot be assembled correctly with many current assembly tools. Therefore, most repeat regions have to be checked manually. If finishing rates are to increase further, most repetitive regions must be assembled correctly and be finished in an automated fashion. The Dupfinisher computer program is designed to finish repeats with minimal human interaction. It can automatically detect repetitive regions, assemble each repeat individually using paired draft reads and primer walk reads, check the quality of these subassemblies, create artificial joins for finished and properly assembled repeats and run automated gap closure scripts on unfinished subassemblies. Dupfinisher is able to solve the majority of repeats in a microbial genome automatically, thus greatly reducing the amount of human attention needed. Dupfinisher has now been used in finishing more than 60 genomes and can be adapted to aid in finishing processes for whole bacterial genome and large insert clone projects.