SSR基因分型器：一种用于全基因组重测序和简化代表性测序项目的简单序列重复基因分型应用程序。

SSRgenotyper: A simple sequence repeat genotyping application for whole-genome resequencing and reduced representational sequencing projects.

作者信息

Lewis Daniel H, Jarvis David E, Maughan Peter J

机构信息

Department of Plant and Wildlife Sciences Brigham Young University Provo Utah 84058 USA.

出版信息

Appl Plant Sci. 2020 Dec 3;8(12):e11402. doi: 10.1002/aps3.11402. eCollection 2020 Dec.

DOI:10.1002/aps3.11402

PMID:33344093

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7742204/

Abstract

PREMISE

Many programs can identify simple sequence repeat (SSR) motifs in genomic data. SSRgenotyper extends SSR identification to en masse genotyping from resequencing data for diversity panels and linkage mapping populations.

METHODS AND RESULTS

SSRgenotyper will find and genotype SSRs from SAM files and an SSR reference FASTA. Several outputs are possible, including a simple table with the SSR marker name, position, and SSR alleles, defined by the repeat number of the repeat motif. Specific output files include a GENEPOP-formatted file for downstream genetic diversity analyses and a traditional A, H, B mapping file output that is phased to the parents of the population for biparental linkage map construction. Linkage maps produced using SSRgenotyper genotypes were highly collinear with physical maps and correctly inferred known phylogenies.

CONCLUSIONS

SSRgenotyper provides an easy-to-use, accurate, and scalable SSR genotyping platform for whole-genome resequencing data. SSRgenotyper is freely available at https://github.com/dlewis27/SSRgenotyper.

摘要

前提

许多程序能够识别基因组数据中的简单序列重复（SSR）基序。SSRgenotyper将SSR识别扩展到从重测序数据中对多样性面板和连锁作图群体进行大规模基因分型。

方法与结果

SSRgenotyper能够从SAM文件和SSR参考FASTA中查找SSR并进行基因分型。它可以生成多种输出，包括一个简单的表格，其中包含SSR标记名称、位置以及由重复基序的重复次数定义的SSR等位基因。特定的输出文件包括一个用于下游遗传多样性分析的GENEPOP格式文件，以及一个传统的A、H、B作图文件输出，该文件已根据双亲连锁图谱构建群体的亲本进行了分型。使用SSRgenotyper基因型生成的连锁图谱与物理图谱高度共线，并正确推断了已知的系统发育关系。