biostudies-literatureLup SDMinisterio de Ciencia e InnovaciónGeneralitat Valenciana1042913https://www.ebi.ac.uk/biostudies/studies/S-EPMC9909543biostudies-literatureUnknown14Mapping-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, F₂, M₂, and M₃ mapping populations, chemically induced mutation and natural Frontiers in plant scienceVersatile mapping-by-sequencing with Easymap v.2.PMC9909543PROMETEO/2019/117, ACIF/2018/005PGC2018-093445-B-I00, PID2021-127725NB-I00Micol JLNavarro-Quiles CLup SDfalseVersatile 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 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, F₂, M₂, and M₃ mapping populations, chemically induced mutation and natural 2023-01-01T00:00:00Z20232026-07-14T18:40:42.766Z2024-11-09T01:30:26.794ZS-EPMC99095433677869210.3389/fpls.2023.1042913