So far I haven't done any variant calling as such. Nanopore I have used for 16s microbiome data.

Now My question/doubt so how do I proceed for nano-pore virus sequencing data


  • I get fast5 files
  • The i perform base-calling using guppy
  • Get fastq files

Now after doing the above is it possible to use variant calling that is used for Ilumina once I get the fastq files?


2 Answers 2


Tools for illumina are not really suitable for long read sequencing. For nanopore data I would suggest LongShot, Clair3 or DeepVariant-PEPPER.


Sure it is possible, but I guess it won't be more reliable than a method specifically designed for Nanopore. But if you use Nanopore I guess accuracy is not your main concern.


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