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 con-tigs. 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.
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