What tools to assess coverage, completeness and contamination?

Question

[Kárita]

What tools can I use to evaluate coverage, completeness and contamination of an assembled genome?

I tried using coverM and checkM but I'm having problems with both, if anyone can help me with others, I'll be grateful!

[GenoMax]

What kind of problems? Prokaryotic or Eukaryotic genome?

BUSCO is a good option: https://busco.ezlab.org/

[Kárita]

Prokaryote genome, I downloaded and installed it via conda but they simply don't run, it always gives an error.

Answer 1

[Mensur Dlakic]

I'm having problems with both

and

but they simply don't run, it always gives an error.

is not really describing your problems. Those programs are well-tested and in frequent use, so there is an expectation that they should work. What makes you think that any program we propose - you already have a link to BUSCO - will work?

So we can help you, it may be more productive to describe exactly what you did and what the error message says. In case you don't want to do that, there is also CheckM2:

https://github.com/chklovski/CheckM2