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)