Huang S, Kang M, Xu A.

Bioinformatics. 2017 Aug 15;33(16):2577-2579. doi:10.1093/bioinformatics/btx220

HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly.

Produces a reference and an alternate assembly. Scaffolding is improved by cross-comparison of the assemblies.