Versatile mapping-by-sequencing with Easymap v.2

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 E...

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Bibliographic Details
Published in:Frontiers in plant science 2023-01, Vol.14, p.1042913-1042913
Main Authors: Lup, Samuel Daniel, Navarro-Quiles, Carla, Micol, José Luis
Format: Article
Language:English
Subjects:
forward genetics
mapping-by-sequencing
next generation sequencing
Plant Science
QTL-seq
variant density mapping
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Summary: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 large DNA insertions. Here, we describe Easymap v.2, which also maps small insertion/deletions (InDels), and includes workflows to perform QTL-seq and variant density mapping analyses. Each mapping workflow can accommodate different experimental designs, including outcrossing and backcrossing, F , M , and M 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.
ISSN:1664-462X
1664-462X
DOI:10.3389/fpls.2023.1042913