I have short reads (Illumina) data with x30-40 depth for several varieties of a plant genome.
A reference genome for the same species exists.
I would like to assemble the reads into pseudomolecules based on the reference genome.
Is anybody aware of an existing tool that can do that?
I've seen a few tools designed to do that with long reads or contigs (e.g. RAGOO), so maybe I should try creating contigs de-novo first, and than use the reference? What tool is capable of dealing with data at this depth?
Thanks a lot!