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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...

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Autores principales: Huang, Shengfeng, Chen, Zelin, Huang, Guangrui, Yu, Ting, Yang, Ping, Li, Jie, Fu, Yonggui, Yuan, Shaochun, Chen, Shangwu, Xu, Anlong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2012
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.
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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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