Question: Reference-guided assembly from short reads
gravatar for liorglic
17 months ago by
liorglic330 wrote:

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!

ngs assembly • 1.1k views
ADD COMMENTlink written 17 months ago by liorglic330

Reference Guided De Novo assembly of Contigs generated from Illumina PE Reads
Reference guided assembly methods

ADD REPLYlink written 17 months ago by genomax91k

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.

ADD REPLYlink written 17 months ago by liorglic330

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?

ADD REPLYlink modified 8 months ago • written 8 months ago by ricardoguerreiro212160

hi Lior,

do you have a solution?

ADD REPLYlink written 5 weeks ago by eitamarsaraf0

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.

ADD REPLYlink written 5 weeks ago by liorglic330

why you didn't use only RagTag? you can align your reads, trimming, exclude unmapped, and then convert bam to fasta

ADD REPLYlink written 5 weeks ago by eitamarsaraf0
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