ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching
Next-generation sequencing (NGS) is a powerful technology as it can produce millions of short read pairs covering whole genome; however, a complete genome assembly remains challenging. Usually, assembled genome pieces (i.e., contigs) are merged into chains (i.e., scaffolds) using read pairs mapped to pairs of contigs. A recent comprehensive evaluation of available software shows that the scaffolding problem is still open . In this paper we present a novel scaffolding tool ScaffMatch based on the maximum weight matching of pairs of reverse complement strands representing contigs and further filling the scaffold with skipped short contigs.
KeywordsRead Pair Scaffolding Tool Maximum Weight Match Bundle Size Short Contigs