text: user285: 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?
  
  user681: Tools for illumina are not really suitable for long read sequencing. For nanopore data I would suggest LongShot, Clair3 or DeepVariant-PEPPER.
  
original_text: 285: <p>So far I haven't done any variant calling as such. Nanopore I have used for 16s microbiome data.</p>
  <p>Now My question/doubt so how do I proceed for nano-pore virus sequencing data</p>
  <p>Steps:</p>
  <ul>
  <li>I get fast5 files</li>
  <li>The i perform base-calling using guppy</li>
  <li>Get fastq files</li>
  </ul>
  <p>Now after doing the above is it possible to use variant calling that is used for Ilumina once I get the fastq files?</p>
   681: <p>Tools for illumina are not really suitable for long read sequencing. For nanopore data I would suggest <a href="https://github.com/pjedge/longshot" rel="nofollow noreferrer">LongShot</a>, <a href="https://github.com/HKU-BAL/Clair3" rel="nofollow noreferrer">Clair3</a> or <a href="https://github.com/kishwarshafin/pepper" rel="nofollow noreferrer">DeepVariant-PEPPER</a>.</p>
  