These are biocomputational tools developed by our program and collaborators through the ‘Tools for Genomic-Assisted Breeding in Polyploids’ USDA-NIFA-SCRI project (Award No. 2020-51181-32156).
Reads2Map
A collection of WDL bioinformatics workflows to benchmark marker quality coming from different pipelines using a linkage map quality as a diagnosis. The workflows perform sequencing reads alignment, SNP calling, genotype/dosage calling, and linkage map building with diverse software and parameters.
https://github.com/Cristianetaniguti/Reads2Map
VIEWpoly
A shiny app and R package for visualizing and exploring results from polyploid genetic analysis using an interactive graphical user interface.
https://github.com/mmollina/viewpoly
Qploidy
An R package for determining copy number variation on high-throughput genotyping platform’s raw data.
https://github.com/Cristianetaniguti/Qploidy