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HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly
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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870766/ https://www.ncbi.nlm.nih.gov/pubmed/28407147 http://dx.doi.org/10.1093/bioinformatics/btx220 |
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author | Huang, Shengfeng Kang, Mingjing Xu, Anlong |
author_facet | Huang, Shengfeng Kang, Mingjing Xu, Anlong |
author_sort | Huang, Shengfeng |
collection | PubMed |
description | 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/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-5870766 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-58707662018-03-29 HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly Huang, Shengfeng Kang, Mingjing Xu, Anlong Bioinformatics Applications Notes 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/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2017-08-15 2017-04-12 /pmc/articles/PMC5870766/ /pubmed/28407147 http://dx.doi.org/10.1093/bioinformatics/btx220 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Applications Notes Huang, Shengfeng Kang, Mingjing Xu, Anlong HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly |
title | HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly |
title_full | HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly |
title_fullStr | HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly |
title_full_unstemmed | HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly |
title_short | HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly |
title_sort | haplomerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870766/ https://www.ncbi.nlm.nih.gov/pubmed/28407147 http://dx.doi.org/10.1093/bioinformatics/btx220 |
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