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aineniamh / snipit

snipit: summarise snps relative to your reference sequence
GNU General Public License v3.0
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Suggestion: enhancements to show possible effects on protein #11

Open martinmchugh opened 2 years ago

martinmchugh commented 2 years ago

This is a great tool for visualsing nucleotide changes, thanks for making it available to the community!

A related use case would be to visualise amino acid changes vs a reference (eg if giving snipit an alignment of a specific CDS of interest), which I don't think is currently supported? Either by giving it the amino acid sequence directly as the input, or by defining the start codon in the ref and converting on the fly.

As an alternative (or complement), it would be nice to be able to highlight nucleotide changes expected to be non-synonymous in the ouput in some way.

Maybe these suggestions don't scale so well to whole genomes which is what I know snipit was initially designed for.

aineniamh commented 5 months ago

Hi @martinmchugh, @ammaraziz has added amino acid alignment support to the tool- so you can now supply amino acid alignments!