├── manual.v3.4.pdf
└── README.md


/manual.v3.4.pdf:
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https://raw.githubusercontent.com/mapleforest/HaploMerger2/HEAD/manual.v3.4.pdf


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/README.md:
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 1 | # HaploMerger2
 2 | 
 3 | HaploMerger2 (HM2) is an important upgrade over HaploMerger.
 4 | 
 5 | 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.
 6 | 
 7 | 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.
 8 | 
 9 | HM2 also implements sensitive assembly error correction, a reliable gap-closing method and a hierarchical scaffolding procedure on haploid assembly.
10 | 
11 | HaploMerger2 is freely available for acadamic use: https://github.com/mapleforest/HaploMerger2/releases/
12 |  
13 | # Citation
14 | 
15 | * Shengfeng Huang, et al. HaploMerger2: rebuilding both haploid sub-assemblies from a heterozygous animal diploid genome assembly. submitted.
16 | 
17 | * Shengfeng Huang, et al. HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies. Genome Res. 2012, 22(8):1581-1588.	
18 | 
19 | 
20 | 


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