HaploMerger2 (HM2) is an important upgrade over HaploMerger.
HM2 is an easy-to-use automated pipeline for improving geneome assembly in the post-assembly stage. It consists of a set of executables as well as wrappers for several third-part software.
It is designed to untangle allelic relations between haplotype sequences in a highly-polymorphic diploid assembly, and then reconstruct and output two separated haploid sub-assemblies, the reference (the better one) and the alternative.
HM2 also implements sensitive assembly error correction, a reliable gap-closing method and a hierarchical scaffolding procedure on haploid assembly.
HaploMerger2 is freely available for acadamic use: https://github.com/mapleforest/HaploMerger2/releases/
Shengfeng Huang, et al. HaploMerger2: rebuilding both haploid sub-assemblies from a heterozygous animal diploid genome assembly. submitted.
Shengfeng Huang, et al. HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies. Genome Res. 2012, 22(8):1581-1588.