HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes

Abstract Background Identifying haplotypes is central to sequence analysis in diploid or polyploid genomes. Despite this, there remains a lack of research and tools designed for physical phasing and its downstream analysis. Results HaplotypeTools is a new toolset to phase variant sites using VCF and...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autor principal:	Rhys A. Farrer
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Haplotype Phasing Recombination Software Batrachochytrium dendrobatidis Hybridization Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/b314ebcffefc47d986805ec89e4c0754
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:b314ebcffefc47d986805ec89e4c0754
record_format	dspace
spelling	oai:doaj.org-article:b314ebcffefc47d986805ec89e4c07542021-11-28T12:11:11ZHaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes10.1186/s12859-021-04473-11471-2105https://doaj.org/article/b314ebcffefc47d986805ec89e4c07542021-11-01T00:00:00Zhttps://doi.org/10.1186/s12859-021-04473-1https://doaj.org/toc/1471-2105Abstract Background Identifying haplotypes is central to sequence analysis in diploid or polyploid genomes. Despite this, there remains a lack of research and tools designed for physical phasing and its downstream analysis. Results HaplotypeTools is a new toolset to phase variant sites using VCF and BAM files and to analyse phased VCFs. Phasing is achieved via the identification of reads overlapping ≥ 2 heterozygous positions and then extended by additional reads, a process that can be parallelized across a computer cluster. HaplotypeTools includes various utility scripts for downstream analysis including crossover detection and phylogenetic placement of haplotypes to other lineages or species. HaplotypeTools was assessed for accuracy against WhatsHap using simulated short and long reads, demonstrating higher accuracy, albeit with reduced haplotype length. HaplotypeTools was also tested on real Illumina data to determine the ancestry of hybrid fungal isolate Batrachochytrium dendrobatidis (Bd) SA-EC3, finding 80% of haplotypes across the genome phylogenetically cluster with parental lineages BdGPL (39%) and BdCAPE (41%), indicating those are the parental lineages. Finally, ~ 99% of phasing was conserved between overlapping phase groups between SA-EC3 and either parental lineage, indicating mitotic gene conversion/parasexuality as the mechanism of recombination for this hybrid isolate. HaplotypeTools is open source and freely available from https://github.com/rhysf/HaplotypeTools under the MIT License. Conclusions HaplotypeTools is a powerful resource for analyzing hybrid or recombinant diploid or polyploid genomes and identifying parental ancestry for sub-genomic regions.Rhys A. FarrerBMCarticleHaplotypePhasingRecombinationSoftwareBatrachochytrium dendrobatidisHybridizationComputer applications to medicine. Medical informaticsR858-859.7Biology (General)QH301-705.5ENBMC Bioinformatics, Vol 22, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Haplotype Phasing Recombination Software Batrachochytrium dendrobatidis Hybridization Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5
spellingShingle	Haplotype Phasing Recombination Software Batrachochytrium dendrobatidis Hybridization Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5 Rhys A. Farrer HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes
description	Abstract Background Identifying haplotypes is central to sequence analysis in diploid or polyploid genomes. Despite this, there remains a lack of research and tools designed for physical phasing and its downstream analysis. Results HaplotypeTools is a new toolset to phase variant sites using VCF and BAM files and to analyse phased VCFs. Phasing is achieved via the identification of reads overlapping ≥ 2 heterozygous positions and then extended by additional reads, a process that can be parallelized across a computer cluster. HaplotypeTools includes various utility scripts for downstream analysis including crossover detection and phylogenetic placement of haplotypes to other lineages or species. HaplotypeTools was assessed for accuracy against WhatsHap using simulated short and long reads, demonstrating higher accuracy, albeit with reduced haplotype length. HaplotypeTools was also tested on real Illumina data to determine the ancestry of hybrid fungal isolate Batrachochytrium dendrobatidis (Bd) SA-EC3, finding 80% of haplotypes across the genome phylogenetically cluster with parental lineages BdGPL (39%) and BdCAPE (41%), indicating those are the parental lineages. Finally, ~ 99% of phasing was conserved between overlapping phase groups between SA-EC3 and either parental lineage, indicating mitotic gene conversion/parasexuality as the mechanism of recombination for this hybrid isolate. HaplotypeTools is open source and freely available from https://github.com/rhysf/HaplotypeTools under the MIT License. Conclusions HaplotypeTools is a powerful resource for analyzing hybrid or recombinant diploid or polyploid genomes and identifying parental ancestry for sub-genomic regions.
format	article
author	Rhys A. Farrer
author_facet	Rhys A. Farrer
author_sort	Rhys A. Farrer
title	HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes
title_short	HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes
title_full	HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes
title_fullStr	HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes
title_full_unstemmed	HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes
title_sort	haplotypetools: a toolkit for accurately identifying recombination and recombinant genotypes
publisher	BMC
publishDate	2021
url	https://doaj.org/article/b314ebcffefc47d986805ec89e4c0754
work_keys_str_mv	AT rhysafarrer haplotypetoolsatoolkitforaccuratelyidentifyingrecombinationandrecombinantgenotypes
_version_	1718408161980841984

HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes

Ejemplares similares