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Currently, the ingest pipeline accepts any format for the strain names.
We should canonicalize them to have prettier names for display in Auspice and to have a way to deduplicate sequences.
Description
We need a clear standard format for strain names. If we follow the existing pattern we use for other pathogens (e.g. SARS-CoV-2), this would be <country>/<sample_id>/<year>
Context
Currently, the ingest pipeline accepts any format for the strain names.
We should canonicalize them to have prettier names for display in Auspice and to have a way to deduplicate sequences.
Description
We need a clear standard format for strain names. If we follow the existing pattern we use for other pathogens (e.g. SARS-CoV-2), this would be
<country>/<sample_id>/<year>
Once we've decided on a format, we should add necessary transforms to ingest/bin/transform-strain-names.
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