# Visualization of mutations in (part of) viral genome - existing tools?

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)

?

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).