Lup Samuel Daniel, Navarro-Quiles Carla, Micol José Luis
Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain.
Front Plant Sci. 2023 Jan 26;14:1042913. doi: 10.3389/fpls.2023.1042913. eCollection 2023.
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.
测序定位法将下一代测序（NGS）与通过连锁分析的经典遗传定位相结合，以建立基因与表型的关系。尽管已经开发了许多工具来分析NGS数据集，但用于测序定位的工具却很少。其中一个工具是Easymap，它是一个多功能、易于使用的软件包，可对点突变和大DNA插入进行自动定位。在这里，我们描述了Easymap v.2，它还可对小插入/缺失（InDels）进行定位，并包括执行QTL-seq和变异密度定位分析的工作流程。每个定位工作流程都可以适应不同的实验设计，包括杂交和回交、F、M和M定位群体、化学诱导突变和自然变异定位、包含基因组或互补DNA序列的单端或双端读数的输入文件，以及FASTQ和VCF格式的替代对照样本文件。在没有定位算法的情况下，Easymap v.2也可以用作变异分析器，并且包括多线程选项。
