AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data

Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly. AFLAP is va...

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Autores principales: Fletcher, Kyle, Zhang, Lin, Gil, Juliana, Han, Rongkui, Cavanaugh, Keri, Michelmore, Richard
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8061198/
https://www.ncbi.nlm.nih.gov/pubmed/33883006
http://dx.doi.org/10.1186/s13059-021-02326-x
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author Fletcher, Kyle
Zhang, Lin
Gil, Juliana
Han, Rongkui
Cavanaugh, Keri
Michelmore, Richard
author_facet Fletcher, Kyle
Zhang, Lin
Gil, Juliana
Han, Rongkui
Cavanaugh, Keri
Michelmore, Richard
author_sort Fletcher, Kyle
collection PubMed
description Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly. AFLAP is validated and contrasted to a conventional workflow using simulated data. AFLAP is applied to whole genome sequencing and genotype-by-sequencing data of F1, F2, and recombinant inbred populations of two different plant species, producing genetic maps that are concordant with genome assemblies. The AFLAP-based genetic map for Bremia lactucae enables the production of a chromosome-scale genome assembly. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02326-x.
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spelling pubmed-80611982021-04-22 AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data Fletcher, Kyle Zhang, Lin Gil, Juliana Han, Rongkui Cavanaugh, Keri Michelmore, Richard Genome Biol Method Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly. AFLAP is validated and contrasted to a conventional workflow using simulated data. AFLAP is applied to whole genome sequencing and genotype-by-sequencing data of F1, F2, and recombinant inbred populations of two different plant species, producing genetic maps that are concordant with genome assemblies. The AFLAP-based genetic map for Bremia lactucae enables the production of a chromosome-scale genome assembly. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02326-x. BioMed Central 2021-04-21 /pmc/articles/PMC8061198/ /pubmed/33883006 http://dx.doi.org/10.1186/s13059-021-02326-x Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Fletcher, Kyle
Zhang, Lin
Gil, Juliana
Han, Rongkui
Cavanaugh, Keri
Michelmore, Richard
AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data
title AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data
title_full AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data
title_fullStr AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data
title_full_unstemmed AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data
title_short AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data
title_sort aflap: assembly-free linkage analysis pipeline using k-mers from genome sequencing data
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8061198/
https://www.ncbi.nlm.nih.gov/pubmed/33883006
http://dx.doi.org/10.1186/s13059-021-02326-x
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