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:

1. Assembling PacBio reads and then using a tool to integrate the two assemblies? Is there anything like this? Which tool would you use?

2. Using a tool that can assemble the genome from both the chromium and the PacBio reads? Is there anything like it? 

3. 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 
Hello again alslonik !

Here I'll add my little pinch of salt and recommend you having a look on that great manual : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100563/ . Of course it was not tested on plant genome, but it help you to orient your choice concerning assembly strategy depending on the technology you used and on your sequencing depth. 

I already saw that you wanted to give it a try to quickmerge so you may have already saw that manual. As I tried quickmerge myself with 2 different PacBio only assembly, I have to say I was really satisfied with the result of quickmerge concerning contiguity and completeness. As you did a Falcon assembly, you can try merging a Falcon assembly and a Canu assembly, it may give some improvement as well, if you have the time of trying that of course !

Cheers,

Roxane