How can you determine ploidy of a genome?

Question

[kristina.mahan]

What tools can give you the ploidy of a genome? I used jellyfish to create a kmer count histogram and used GenomeScope to visualize the kmer histogram. GenomeScope tells you: Heterozygosity, Genome Haploid Length, Genome Repeat Length, Genome Unique Length, Model Fit, and Read Error Rate. How can you use this info and the kmer peaks to determine ploidy?

Answer 1

[h.mon]

GenomeScope FAQ says it can't be used to estimate ploidy, see the FAQ:

Q: Can GenomeScope be used to estimate ploidy, or used with genomes with higher ploidy?

A: No, GenomeScope is only appropriate for diploid genomes. In principle the model could be extend to higher levels of polyploidy by extending the model to consider additional peaks in the k-mer profile, but this is not currently supported.

You may try SmudgePlot, see GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes.