Filter contigs by depth

[termithorbor]

Hi,

I want to run a Breseq analysis and therfore I need to filter the contigs in my assembly by depth.
is this somehow possible in Unicycler?

Thanks :)

Here is a short description what I want to do/need:
Yes, breseq can analyze input reference sequences containing multiple fragments, like what you typically have after an incomplete de novo assembly.

IMPORTANT: Use the --contig-reference|-c option instead of -r for passing an entire file from a de novo assembly in which all contigs should have the same coverage. If you have a plasmid and chromosome, put each in a different file and pass the -c option twice, so coverage is only assumed to be the same within each input file.