<p>I ended up using <code>lolliplots</code> from the <a href="https://bioconductor.org/packages/devel/bioc/vignettes/trackViewer/inst/doc/trackViewer.html" rel="nofollow noreferrer">trackViewer R package</a>; it can do VCF-based visualization <em>and</em> is flexible enough I can feed it data from other sources (I wound up parsing Nextclade mutation calls for the amino acids since I had these anyway).</p>

CC BY-SA 4.0
2022-02-27T02:55:57.700Z
Thanks for your update, this really useful. The Vignette package I do recognise, it does look really cool
M__
CC BY-SA 4.0
2022-01-27T13:46:19.433Z
2022-01-27T13:46:19.433Z
KeyboardCat
<p>I'm trying to visualize mutations in SARS-CoV-2 sequences, somewhat like it's done on outbreak.info:
<a href="https://i.sstatic.net/ziBPR.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/ziBPR.png" alt="An overview of mutations in the B.1.617.2 lineage, shown as dots labeled with amino acids on a horizontal bar divided by genes." /></a></p>
<p>but for individual sequences, probably on the base of the vcf files generated by the <a href="https://github.com/artic-network/fieldbioinformatics" rel="nofollow noreferrer">ARTIC pipeline</a>. A pipeline focused on virus nanopore output.</p>
<p>The ready-made tools I've found for visualization of mutations so far were specifically tailored to human sequences and/or for visualizing aggregated data for multiple genomes, or were web tools, which can't be used for medical data due to confidentiality.</p>
<p>Is there any existing offline tool that</p>
<ul>
<li>is Linux-based</li>
<li>can be integrated into an automated pipeline</li>
<li>is tailored towards viral genomes or is &quot;organism-agnostic&quot;</li>
<li>is based on comparing an individual sequence to a reference sequence</li>
<li>shows the sequence as &quot;blocks&quot; of genes with the mutations highlighted</li>
<li>(ideally plays well with MultiQC for integration into an existing report, but that's a nice-to-have)</li>
</ul>
<p>?</p>

<vcf><visualization><covid-19><software-recommendation><sars-cov-2>
Visualization of mutations in (part of) viral genome - existing tools?
# Visualization of mutations in (part of) viral genome - existing tools?

(Asked by: username_0 on 2021-12-17)

I'm trying to visualize mutations in SARS-CoV-2 sequences, somewhat like it's done on outbreak.info:
[![An overview of mutations in the B.1.617.2 lineage, shown as dots labeled with amino acids on a horizontal bar divided by genes.](https://i.sstatic.net/ziBPR.png)](https://i.sstatic.net/ziBPR.png)

but for individual sequences, probably on the base of the vcf files generated by the [ARTIC pipeline](https://github.com/artic-network/fieldbioinformatics). A pipeline focused on virus nanopore output.

The ready-made tools I've found for visualization of mutations so far were specifically tailored to human sequences and/or for visualizing aggregated data for multiple genomes, or were web tools, which can't be used for medical data due to confidentiality.

Is there any existing offline tool that

* is Linux-based
* can be integrated into an automated pipeline
* is tailored towards viral genomes or is "organism-agnostic"
* is based on comparing an individual sequence to a reference sequence
* shows the sequence as "blocks" of genes with the mutations highlighted
* (ideally plays well with MultiQC for integration into an existing report, but that's a nice-to-have)

?

**Tags:** vcf, visualization, covid-19, software-recommendation, sars-cov-2

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## 1 answers

### Answer by username_0 on 2022-01-27. Score: 3 | Accepted answer

I ended up using `lolliplots` from the [trackViewer R package](https://bioconductor.org/packages/devel/bioc/vignettes/trackViewer/inst/doc/trackViewer.html); it can do VCF-based visualization *and* is flexible enough I can feed it data from other sources (I wound up parsing Nextclade mutation calls for the amino acids since I had these anyway).

> **Comments:**
> **username_1**: Thanks for your update, this really useful. The Vignette package I do recognise, it does look really cool  

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