Journal
BIOINFORMATICS
Volume 33, Issue 16, Pages 2577-2579Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btx220
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Funding
- 973 Project [2013CB835305]
- National Nature Science Fund [31171193]
- National Supercomputer Center in Guangzhou
- NSFC-Guangdong Joint Fund
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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/.
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