text: user12755: I'm trying to visualize mutations in SARS-CoV-2 sequences, somewhat like it's done on outbreak.info:
  
  but for individual sequences, probably on the base of the vcf files generated by the ARTIC pipeline. 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)
  
  ?
  
  user12755: I ended up using lolliplots from the trackViewer R package; 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).
  
original_text: 12755: <p>I'm trying to visualize mutations in SARS-CoV-2 sequences, somewhat like it's done on outbreak.info:
  <a href="https://i.stack.imgur.com/ziBPR.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/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>
   12755: <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>
  