Can any long read assemblers incorporate both nanopore and pacbio reads in the same run?

Question

[O.rka]

I have acquired genomic reads from nanopore and pacbio technologies for a diatom lacking a reference sequence.

I want to build a good reference assembly and would like to incorporate both nanopore and pacbio reads in the same run.

If this is not possible, is there a way to get a consensus assembly from 2 separate assemblies?

Bonus: I also have A LOT of RNA-seq data for this diatom. Is it possible to use this to "polish" the genomic scaffolds? I know polishing is usually using shotgun genomics but I'm wondering if there is a way to use these RNA-seq datasets in the same way? I don't expect there to be many introns but there are some...this may make it difficult/impossible to reliably use RNA-seq data.

[GenoMax]

flye can handle both (https://github.com/fenderglass/Flye ) not sure if at the same time.

[O.rka]

I'm doing a flye run for the nanopore data right now. It wasn't able to handle both at the same time. It also required a --genome-size which is difficult since this is de-novo.

[GenoMax]

Looks like you had asked a very similar question a couple of weeks back and did get an answer there. Did `canu` not work?

• Is it possible to use genomic reads from PacBio and Nanopore with Illumina RNA-seq reads for de-novo assembly?

[O.rka]

My apologies, when I started writing this question it seemed different and then it slowly turned into the last question as I added more text. I will try not to do this again.

[Insafnaser]

I am actually doing the same work now! trying to assemble nanopore, Pacbio and Illumina reads for a diatom without a reference genome. Can I know how did it work out for you and whether were you able to submit the assembly and do some work on it? Would be very helpful to me to know this before I start working on it? Thank you!

Answer 1

[h.mon]

There isn't much difference between your question from two weeks ago and this one, so I think my previous answer still holds (see also Flye mentioned by genomax):

I know at least Canu can use PacBio and NanoPore reads simultaneously to assemble a genome - there may be other assemblers out there capable of mixing PabBio and NanoPore input data.

After assembly, you may use Pilon with the RNAseq data to polish the draft assembly, see Using pilon with RNAseq data #50, Racon may also work.

In addition to my old answer:

If this is not possible, is there a way to get a consensus assembly from 2 separate assemblies?

Search for "assembly reconciliation" tools.

[O.rka]

I didn’t realize how similar this question was as I was writing it. Thank you for answering this. I’m going to try out the suggestions in your answer once I can get everything installed.