Answers.Body: <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>
  
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Answers.CreationDate: 2021-12-06T20:47:49.377Z
Answers.LastActivityDate: 2021-12-06T20:47:49.377Z
Answers.UserDisplayName: Wouter De Coster
Answers.Body: <p>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.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-12-06T19:08:38.120Z
Answers.LastActivityDate: 2021-12-06T19:08:38.120Z
Answers.UserDisplayName: juanjo75es
Body: <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>
  
Tags: <variant-calling><nanopore>
Title: Nanopore variant calling
ThreadText: # Nanopore variant calling
  
  (Asked by: username_0 on 2021-12-06)
  
  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?
  
  **Tags:** variant-calling, nanopore
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2021-12-06. Score: 1 | Accepted answer
  
  Tools for illumina are not really suitable for long read sequencing. For nanopore data I would suggest [LongShot](https://github.com/pjedge/longshot), [Clair3](https://github.com/HKU-BAL/Clair3) or [DeepVariant-PEPPER](https://github.com/kishwarshafin/pepper).
  
  
  ---
  
  ### Answer by username_2 on 2021-12-06. Score: -1
  
  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.
  
  
  ---
  
  