Dataset Information
HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly.
Ontology highlight
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-closing method for haploid sub-assemblies. Using HM2, we demonstrate that two haploid sub-assemblies reconstructed from a real, highly-polymorphic diploid assembly show greatly improved continuity.Availability and implementation
Source code, executables and the testing dataset are freely available at https://github.com/mapleforest/HaploMerger2/releases/.Contact
hshengf2@mail.sysu.edu.cn.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Huang S
PROVIDER: S-EPMC5870766 | biostudies-literature | 2017 Aug
REPOSITORIES: biostudies-literature
Publications
HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly.
Bioinformatics (Oxford, England) 20170801 16
<h4>Summary</h4>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. HM ...[more]