Thank you very much for the clarification!
I came across a list of criteria that NCBI uses to select reference genomes, which includes CheckM completeness among other factors, but I couldn't find whether there is a defined cutoff value that an assembly must meet to be considered eligible.
Does anyone know if NCBI uses a specific threshold for CheckM completeness for a reference genome selection? Or is it purely comparative across available assemblies for a given species?
2 answers
It appears there is no strict threshold, but it depends on how many other assemblies for a given taxa are already submitted. I think their logic is it's okay to accept a lower quality genome if it's covering gaps in taxonomy until better ones come along.
In their prokaryotic release notes, this is what it says:
Added CheckM completeness cut-offs to validate annotation. An annotated assembly will only be added to the RefSeq collection if it meets the following criteria:
For species with more than 1000 assemblies in RefSeq, the completeness is higher than the species Average Completeness - 3 times the standard deviation . For species with 10-1000 assemblies in RefSeq, the completeness is higher than the smaller of 90% or the species Average Completeness - 3 times the standard deviation . No CheckM cutoff is applied if there are less than 10 assemblies in the species.
And with their documentation on selecting a genome, it appears CheckM is not considered for eukaryotic genomes.
RefSeq prokaryotic genomes are selected based on the criteria mentioned on this page: https://www.ncbi.nlm.nih.gov/refseq/about/prokaryotes/
For CheckM above page lists following criteria:
In order, assemblies with the highest quantized level of completeness (98 to 100) are preferred over assemblies in the 95-98, 90-95, 85-90, 70-85, 50-70, and under 50 percent level of completeness, as determined by CheckM.
RefSeq genome selection for eukaryotes is based on: https://www.ncbi.nlm.nih.gov/datasets/docs/v2/policies-annotation/genome-processing/refseq-selection/
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