RT Journal Article SR Electronic T1 Versatile mapping-by-sequencing with Easymap v.2 JF bioRxiv FD Cold Spring Harbor Laboratory SP 2022.07.14.500089 DO 10.1101/2022.07.14.500089 A1 Samuel Daniel Lup A1 Carla Navarro-Quiles A1 José Luis Micol YR 2022 UL http://biorxiv.org/content/early/2022/07/14/2022.07.14.500089.abstract AB 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.esCompeting Interest StatementThe authors have declared no competing interest.NGSnext-generation sequencingEMSethyl methanesulfonateSNPsingle-nucleotide polymorphismQTLquantitative trait lociVCFVariant Call Format