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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.

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)

?

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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).

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  • $\begingroup$ Thanks for your update, this really useful. The Vignette package I do recognise, it does look really cool $\endgroup$
    – M__ ♦
    Feb 27, 2022 at 2:55

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