HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly.

ABSTRACT:

Summary

De novo assembly is a difficult issue for heterozygous diploid genomes. The advent of high-throughput short-read and long-read sequencing technologies provides both new challenges and potential solutions to the issue. Here, we present HaploMerger2 (HM2), an automated pipeline for rebuilding both haploid sub-assemblies from the polymorphic diploid genome assembly. It is designed to work on pre-existing diploid assemblies, which are typically created by using de novo assemblers. HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a hierarchical scaffolding procedure and a reliable gap-cl

SUBMITTER: Huang S 

PROVIDER: S-EPMC5870766 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature