BUSCO vs CheckM, which is best for determining bacterial genome completness.

Question

[robert.murphy]

I have 21 bacterial isolates from termite guts and I want to determine the completness of the genomes. Which tool between BUSCO and CheckM is best to do this?

Answer 1

[Mensur Dlakic]

I use CheckM and haven't tried BUSCO in couple of years, so take that into account when considering my advice.

My impression was that BUSCO was too stringent in how it defined completeness and that they didn't use enough reference groups. That might have changed with version 4 of BUSCO based on the increased number of taxonomic groups, but I have no first-hand experience with the latest release. I think CheckM is easy to install and its results are straightforward, though it does require large memory. It is also my impression that CheckM is more or less the standard for prokaryotes (does not work with eukaryotes), while BUSCO may be more useful for eukaryotes even though it works with both. In the long run, BUSCO might overtake CheckM because it is broader in scope and appears to be actively maintained.

[robert.murphy]

Thank you this advice, it is helpful :)