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Optimal strategy for hybrid (Illumina + ONT) assembly #829

Answered by andrewprzh
MaestSi asked this question in Q&A
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Hi!

We have not tried this tool in combination with rnaSPAdes assembly. However, it seems like you may give it a try.
And yes, you are absolutely right, detected FL reads are better be provided with --fl-rna option.

If you have time and a way to evaluate quality of your assembly, I'd suggest to try different pipelines:

  • give rnaSPAdes raw ONT reads (--nanopore)
  • give rnaSPAdes FL cDNA reads obtained with pychopper (--fl-rna)
  • give both sets of reads using respective options.

Best
Andrey

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