Entering edit mode
5.6 years ago
liorglic
★
1.4k
Hello,
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!
Reference Guided De Novo assembly of Contigs generated from Illumina PE Reads
Reference guided assembly methods
Thanks, I've seen these posts, but this still doesn't answer my question, so I'd still like to get some more relevant and up-to-date advise if anyone has one.
I would say so. Try your best assembly possible and then feed it to RaGOO with the reference. I'm trying this right now.
Did you do it? How does it work for you?
hi Lior,
do you have a solution?
Unfortunately no. I do de novo assembly (I use SPAdes) and then scaffold contigs into pseudomolecules using RagTag (successor of RaGOO). Works pretty well for me in most cases.
why you didn't use only RagTag? you can align your reads, trimming, exclude unmapped, and then convert bam to fasta