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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.
SUBMITTER: Lewis DH
PROVIDER: S-EPMC7742204 | biostudies-literature | 2020 Dec
REPOSITORIES: biostudies-literature
Lewis Daniel H DH Jarvis David E DE Maughan Peter J PJ
Applications in plant sciences 20201203 12
<h4>Premise</h4>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.<h4>Methods and results</h4>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 mo ...[more]