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Question: Reference-guided assembly from short reads
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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!

ADD COMMENTlink 9 months ago liorglic • 50
Entering edit mode

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 9 months ago
• 50

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