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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

Steps:

  • 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?

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

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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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