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HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies
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 dipl...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3409271/ https://www.ncbi.nlm.nih.gov/pubmed/22555592 http://dx.doi.org/10.1101/gr.133652.111 |
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author | Huang, Shengfeng Chen, Zelin Huang, Guangrui Yu, Ting Yang, Ping Li, Jie Fu, Yonggui Yuan, Shaochun Chen, Shangwu Xu, Anlong |
author_facet | Huang, Shengfeng Chen, Zelin Huang, Guangrui Yu, Ting Yang, Ping Li, Jie Fu, Yonggui Yuan, Shaochun Chen, Shangwu Xu, Anlong |
author_sort | Huang, Shengfeng |
collection | PubMed |
description | 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 curation when applied to real polymorphic assemblies (e.g., 4%–5% heterozygosity). We also used HaploMerger to analyze the diploid assembly of a single Chinese amphioxus (Branchiostoma belcheri) and compared the resulting haploid assemblies with EST sequences, which revealed that the two haplotypes are not only divergent but also highly complementary to each other. Taken together, we have demonstrated that HaploMerger is an effective tool for analyzing and exploiting polymorphic genome assemblies. |
format | Online Article Text |
id | pubmed-3409271 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-34092712013-02-01 HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies Huang, Shengfeng Chen, Zelin Huang, Guangrui Yu, Ting Yang, Ping Li, Jie Fu, Yonggui Yuan, Shaochun Chen, Shangwu Xu, Anlong Genome Res Resource 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 curation when applied to real polymorphic assemblies (e.g., 4%–5% heterozygosity). We also used HaploMerger to analyze the diploid assembly of a single Chinese amphioxus (Branchiostoma belcheri) and compared the resulting haploid assemblies with EST sequences, which revealed that the two haplotypes are not only divergent but also highly complementary to each other. Taken together, we have demonstrated that HaploMerger is an effective tool for analyzing and exploiting polymorphic genome assemblies. Cold Spring Harbor Laboratory Press 2012-08 /pmc/articles/PMC3409271/ /pubmed/22555592 http://dx.doi.org/10.1101/gr.133652.111 Text en © 2012, Published by Cold Spring Harbor Laboratory Press This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/. |
spellingShingle | Resource Huang, Shengfeng Chen, Zelin Huang, Guangrui Yu, Ting Yang, Ping Li, Jie Fu, Yonggui Yuan, Shaochun Chen, Shangwu Xu, Anlong HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies |
title | HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies |
title_full | HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies |
title_fullStr | HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies |
title_full_unstemmed | HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies |
title_short | HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies |
title_sort | haplomerger: reconstructing allelic relationships for polymorphic diploid genome assemblies |
topic | Resource |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3409271/ https://www.ncbi.nlm.nih.gov/pubmed/22555592 http://dx.doi.org/10.1101/gr.133652.111 |
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