Visualise genetic distance from reference

artic-network / rampart

Read Assignment, Mapping, and Phylogenetic Analysis in Real Time

GNU General Public License v3.0

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Visualise genetic distance from reference #32

Closed rambaut closed 4 years ago

rambaut commented 5 years ago

The call to MiniMap2 in map_single_fastq.py returns the %similarity to the mapped reference. It would be good to be able to include this as a chart in each sample panel (either for the majority mapping or selecting a specific reference).

jameshadfield commented 5 years ago

I wonder if we should just call the SNPs and draw a quick tree with the reference panel + samples?

rambaut commented 5 years ago

I don't think so. It would add new layers of complexity. Ultimately, when we make RAMPART more modular, then this sort of thing could be added but at the moment I think we should focus on it being a tool for diagnosing sequencing issues and looking at performance.

rambaut commented 5 years ago

It would just be useful to know how close the reads are to to their best mapping reference (this information is being returned by the mapping script).

jameshadfield commented 4 years ago

Prototype now implemented in 53aa9acf911af565c488ed308f8484e24bf8ad6b

The panel placement hasn't been given much thought & the presence of unmapped having similarity values is somewhat worrying 🤦‍♂

jameshadfield commented 4 years ago

The unmapped 🐛 is fixed -- it was caused by ambiguous mapping results being labeled as unmapped. We no longer store similarities for these reads.