Qploidy is an R package designed for ploidy and aneuploidy estimation using genotyping platform data.
The Qploidy approach is effective under the following conditions:
- Your marker data originates from Axiom or Illumina genotyping arrays.
- Your marker data is derived from targeted sequencing platforms (e.g., DArTag, GTseq, AgriSeq).
- All DNA samples were prepared following the same library preparation protocol.
- You know the ploidy of at least a subset of 60 samples or you know the most common ploidy in the dataset.
- Your dataset includes heterozygous samples.
The methodology will not be effective under the following circumstances:
- Your marker data comes from RADseq or GBS (Genotyping-by-Sequencing) platforms.
- You intend to combine datasets from different sequencing batches.
- For example: If you extracted DNA and sequenced two plates (192 samples) as one batch, and later sequenced an additional three plates (288 samples) as a second batch, you would need to analyze the two batches separately in
Qploidy. Combining all 480 samples into a single analysis will lead to incorrect results.
- For example: If you extracted DNA and sequenced two plates (192 samples) as one batch, and later sequenced an additional three plates (288 samples) as a second batch, you would need to analyze the two batches separately in
- You do not have a subset of samples with known ploidy or lack a predominant ploidy in your dataset.
- Your samples consist of inbred lines (homozygous individuals).
#install.packages("devtools")
devtools::install_github("cristianetaniguti/Qploidy")Qploidytutorial for directions on how to run
If you find a bug or want an enhancement, please submit an issue here.
Taniguti, C.H; Lau, J.; Hochhaus, T.; Arias Lopez, D. C.; Hokanson, S.C.; Zlesak, D. C.; Byrne, D. H.; Klein, P.E. and Riera-Lizarazu, O. Exploring Chromosomal Variations in Garden Roses: Insights from High-density SNP Array Data and a New Tool, Qploidy. Submitted.
This work is funded in part by the Robert E. Basye Endowment in Rose Genetics, Dept. of Horticultural Sciences, Texas A&M University, and USDA’s National Institute of Food and Agriculture (NIFA), Specialty Crop Research Initiative (SCRI) projects: ‘‘Tools for Genomics-Assisted Breeding in Polyploids: Development of a Community Resource’’ (Award No. 2020-51181-32156); and ‘‘Developing Sustainable Rose Landscapes via Rose Rosette Disease Education, Socioeconomic Assessments, and Breeding RRD-Resistant Roses with Stable Black Spot Resistance’’ (Award No. 2022-51181-38330).