SILP3: Maximum likelihood approach to scaffolding

Scaffolding is the important stage of genome assembly consisting of orienting and ordering contigs based on read pairs. We present a scalable scaffolding algorithm that finds most likely contig orientation using integer linear program solved by a non-serial dynamic programming approach. We then formulate the problem of finding most likely contig ordering as an optimization problem and propose a novel ordering algorithm improving over our previous scaffolding tool SILP2.