How can you determine ploidy of a genome?
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14 months ago

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?

ploidy kmer genomescope jellyfish • 644 views
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14 months ago
h.mon 33k

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.

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