Poster: Accurate scaffolding of large genomes using integer programming and Non-Serial Dynamic Programming

The precipitous drop in sequencing costs has generated much enthusiasm for very large scale genome sequencing initiatives. However, assembling high-quality genome sequences from the short reads currently generated by high-throughput sequencing (HTS) technologies represents a formidable computational challenge that has yet to be met. In this work we address the scaffolding step of genome assembly pipelines, whereby sets of assembled contigs are oriented, ordered, and combined into larger structures called scaffolds. Scaffolding is a critical step of practical genome assembly, as the larger structures significantly increase the usefulness of assembled genomes to biologists.