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Haplomerger2 website  

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.

Environment Modules

Run module spider Haplomerger2 to find out what environment modules are available for this application.

System Variables

  • HPC_HAPLOMERGER2_DIR - installation directory
  • HPC_HAPLOMERGER2_BIN- executable directory


If you publish research that uses Haplomerger2 you have to cite it as follows:

Shengfeng Huang, et al. HaploMerger2: rebuilding both haploid sub-assemblies from a heterozygous animal diploid genome assembly. submitted.