Scaffolding is among the most difficult problems in genome assembly. Hapsembler group has an interesting paper on scaffolding that is worth taking a look. We have not gone through it yet, but posting the link here to come back to the topic in future. Abstract below.
We present SCARPA, a novel scaffolder which combines fixed-parameter tractable and bounded algorithms with Linear Programming to produce near- optimal scaffolds. We test SCARPA on real datasets in addition to a simulated diploid genome and compare its performance to several state-of-the-art scaffolders. We show that SCARPA produces longer or similar length scaffolds that are highly accurate compared to other scaffolders. SCARPA is also capable of detecting misassembled contigs and reports them during scaffolding.
Code is available here.