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HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies.

Genome research - 1 Aug 2012

Huang Shengfeng, Chen Zelin, Huang Guangrui, Yu Ting, Yang Ping, Li Jie, Fu Yonggui, Yuan Shaochun, Chen Shangwu, Xu Anlong

Abstract excerpt

Whole-genome shotgun assembly has been a long-standing issue for highly polymorphic genomes, and the advent of next-generation sequencing technologies has made the issue more challenging than ever. Here we present an automated pipeline, HaploMerger, for reconstructing allelic relationships in a diploid assembly. HaploMerger combines a LASTZ-ChainNet alignment approach with a novel graph-based structure, which...

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Identifiers

PMID: 22555592
DOI: 10.1101/gr.133652.111
PMCID: PMC3409271

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