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SSRgenotyper: A simple sequence repeat genotyping application for whole-genome resequencing and reduced
Daniel H Lewis1, David E Jarvis1, Peter J Maughan1
1Department of Plant and Wildlife Sciences Brigham Young University Provo Utah 84058 USA.
Applications in Plant Sciences
|December 21, 2020
Summary
SSRgenotyper enables high-throughput genotyping of simple sequence repeats (SSRs) from whole-genome resequencing data. This tool accurately identifies SSRs for genetic diversity and linkage map construction in various populations.
Area of Science:
- Genomics
- Bioinformatics
- Population Genetics
Background:
- Simple Sequence Repeats (SSRs) are valuable genetic markers.
- Existing tools primarily focus on SSR identification, not large-scale genotyping.
- Resequencing data offers rich genomic information for marker analysis.
Purpose of the Study:
- To introduce SSRgenotyper, a novel platform for SSR genotyping.
- To enable efficient analysis of SSRs from whole-genome resequencing data.
- To support diversity panel and linkage mapping population studies.
Main Methods:
- SSRgenotyper processes SAM files and a FASTA reference for SSR identification and genotyping.
- The tool generates various outputs, including allele data based on repeat numbers.
- Specialized outputs include GENEPOP format for diversity analysis and phased mapping files for linkage construction.
Main Results:
- SSRgenotyper accurately genotypes SSRs from resequencing data.
- Generated linkage maps showed high collinearity with physical maps.
- The tool successfully inferred known phylogenies, validating its accuracy.
Conclusions:
- SSRgenotyper offers a user-friendly, accurate, and scalable solution for SSR genotyping.
- It is well-suited for analyzing whole-genome resequencing data.
- The software is freely available for research use.
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