nanopore-Illumina hybrid RNA assembly

Question

[fabbri.marco]

I am planning to run nanopore-Illumina hybrid assembly. I work with plant. I have run some RNA sequencing with Illumina and some with nanopore. I read that with rnaspdes is possible to assemble Illumina and nanopore fastq in the same run. Any suggestions or comments?

Thank you

Marco

[Madelaine Gogol]

I recently heard of someone using Pilon for something similar, might be another option to consider. There are a few posts on the nanopore community about it.

[Shiyi]

Pilon is great, use long reads and run first, then using Illumina is polish the small SNP, indels. Why RNA assembly? RNA vrius?