Some questions about NCBI archaeal genomes predicted as Low-quality draft

[chklovski]

Some questions about NCBI archaeal genomes predicted as Low-quality draft

[donovan-h-parks]

Hi,

A genome being in RefSeq does not necessarily imply an assembly is of good quality though NCBI makes a best effort to achieve this. I spot checked a few genomes using CheckM v1 which also indicates these genomes are incomplete:

GCF_000372505.1: 3.74%
GCF_000192595.1 3.74%
GCF_000192615.1: 17.6%
GCF_000382765.1: 26.2%

It is possible CheckM v1 and v2 are both incorrect though these are independent methods for estimating genome quality. At least some of these genomes are now recognized at NCBI as being partial and have been suppressed from RefSeq, e.g.:
https://www.ncbi.nlm.nih.gov/assembly/GCF_000372505.1/
https://www.ncbi.nlm.nih.gov/assembly/GCF_000382765.1/.

Hope this helps.

Cheers,
Donovan

[ZongzhiWu]

Many thanks! Really helpful to me.