<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>

CC BY-SA 4.0
2021-12-06T20:47:49.377Z
2021-12-06T20:47:49.377Z
Wouter De Coster
<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>

CC BY-SA 4.0
2021-12-06T19:08:38.120Z
2021-12-06T19:08:38.120Z
juanjo75es
<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>

<variant-calling><nanopore>
Nanopore variant calling
# 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

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## 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).


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### 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.


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