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