HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies.

ABSTRACT: 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 helps to untangle allelic relationships between two haplotypes and guides the subsequent creation of reference haploid assemblies. The pipeline provides flexible parameters and schemes to improve the contiguity, continuity, and completeness of the reference assemblies. We show that HaploMerger produces efficient and accurate results in simulations and has advantages over manual curati

SUBMITTER: Huang S 

PROVIDER: S-EPMC3409271 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature