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Versatile mapping-by-sequencing with Easymap v.2

View ORCID ProfileSamuel Daniel Lup, View ORCID ProfileCarla Navarro-Quiles, View ORCID ProfileJosé Luis Micol
doi: https://doi.org/10.1101/2022.07.14.500089
Samuel Daniel Lup
Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
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Carla Navarro-Quiles
Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
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José Luis Micol
Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
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  • ORCID record for José Luis Micol
  • For correspondence: jlmicol@umh.es
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ABSTRACT

Motivation Mapping-by-sequencing combines Next Generation Sequencing (NGS) with classical genetic mapping by linkage analysis to establish gene-to-phenotype relationships. Although numerous tools have been developed to analyze NGS datasets, only a few are available for mapping-by-sequencing. One such tool is Easymap, a versatile, easy-to-use package that performs automated mapping of point mutations and small insertion/deletions (InDels), as well as large DNA insertions.

Results Here, we describe Easymap v.2, which includes additional workflows to perform QTL-seq and variant density mapping analyses. Each mapping workflow can accommodate different experimental designs, including outcrossing and backcrossing, F2, M2, and M3 mapping populations, chemically induced mutation and natural variant mapping, input files containing single-end or paired-end reads of genomic or complementary DNA sequences, and alternative control sample files in FASTQ and VCF formats. Easymap v.2 can also be used as a variant analyzer in the absence of a mapping algorithm and includes a multi-threading option.

Availability and implementation Code is available at http://genetics.edu.umh.es/resources/easymap/

Contact jlmicol{at}umh.es

Competing Interest Statement

The authors have declared no competing interest.

  • Abbreviations

    NGS
    next-generation sequencing
    EMS
    ethyl methanesulfonate
    SNP
    single-nucleotide polymorphism
    QTL
    quantitative trait loci
    VCF
    Variant Call Format
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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    Posted July 14, 2022.
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    Versatile mapping-by-sequencing with Easymap v.2
    Samuel Daniel Lup, Carla Navarro-Quiles, José Luis Micol
    bioRxiv 2022.07.14.500089; doi: https://doi.org/10.1101/2022.07.14.500089
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    Versatile mapping-by-sequencing with Easymap v.2
    Samuel Daniel Lup, Carla Navarro-Quiles, José Luis Micol
    bioRxiv 2022.07.14.500089; doi: https://doi.org/10.1101/2022.07.14.500089

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