Hello clever community!
I need your advice. I am working on a de novo plant genome assembly of ~400 Mb. I have Chromium 10x data, which was assembled with supernova. I also have Illumina paired end reads. Now I have additional data of PacBio reads, 120x roughly. The genome is diploid and I am thinking about using Falcon.
What do you think should be the best strategy:
Assembling PacBio reads and then using a tool to integrate the two assemblies? Is there anything like this? Which tool would you use?
Using a tool that can assemble the genome from both the chromium and the PacBio reads? Is there anything like it?
Assembling the PacBio reads and using chromium 10x and the illumina for polishing? If I assemble with Falcon, what tool should I use for polishing?
4? Anything else that I am missing to get the best out of what I can get?
Thank you very much in advance! Alex