Hi !

I wonder, do you have a favorite tool to check the quality of an assembly ? I am interested in knowing if there are some real issues (such as chimeric contigs that I should break).

The problem with QUAST is that it depends on a reference (that I don't have of course) .

I came accross CRAQ https://www-nature-com.insb.bib.cnrs.fr/articles/s41467-023-42336-w but I find it a bit difficult to understand. But also Nucbreak, much simpler doi: 10.1186/s12859-020-3414-0. The problem is that I am not sure what it actually does because the paper is more about performance than algorithm.

Do you know of any other ? Thanks !