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nextstrain / auspice

Web app for visualizing pathogen evolution
https://docs.nextstrain.org/projects/auspice/
GNU Affero General Public License v3.0
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Make strain mutation data available via file download and/or API GET request #1052

Closed cornhundred closed 4 years ago

cornhundred commented 4 years ago

Context
Thanks for the great resource. We would like to try and visualize this data using our interactive heatmap Clustergrmmer2 - e.g. a heatmap with strains as columns (with clade categories, and hierarchically clustered using phylogenetic tree) and mutations/metadata as rows linked to a world map. We have a similar example set up using Citibike data here https://github.com/cornhundred/citibike-clustergrammer2 and see GIF below:

small_gif

Description
We would like to obtain the mutation data (nucleotide and AA) for the strains in order to generate the heatmap, but the current downloads do not appear to include this information (e.g. nextstrain_ncov_global_metadata.tsv).

Examples
The mutation data is available on mouseover in the application.

Possible solution
The mutation data could be made available in the metadata as an additional column (e.g. semi colon separated list of mutations that show up on mouseoer). Also, this latest data could be made available via an API.

jameshadfield commented 4 years ago

Hey Nicolas. I understand your desire here. To obtain this information please register with GISAID to obtain the original genomic data & please adhere to their conditions of data sharing when using GISAID data. You are most welcome to run our ncov pipeline to align & identify mutations in the data. Good luck!

cornhundred commented 4 years ago

Ok, thanks for the help :D