Heterozygous genome size estimation using k-mer analysis

Question

[avnim]

In k-mer analysis of heterozygous genome (if the case is similar to that of image linked), i wanted to know, whether the heterozygous peak or the homozygous peak is considered for genome size estimation.

Answer 1

[grant.hovhannisyan]

look here https://www.ncbi.nlm.nih.gov/pubmed/27131372

[avnim]

thanks for the suggestion. We have already assembled the genome and want to know the expected size of genome assembly using kmer analysis hence which peak should be considered for genome size estimation, heterozygous peak or homozygous peak as the heterozygous peak is higher than the homozygous peak.

[grant.hovhannisyan]

not an answer to your question, but you might (heavily) overestimate the size of the heterozygous genome if you assemble it with usual pipelines, because they might assemble heterozygous regions into separate scaffolds. The pipeline above takes this into accounts and also provides some useful metrics.