Geography: will augur recognize correct region if the correct country is provided?

Help and Getting Started
1

Hi there,

In preparing my metadata for an avian influenza build, I have location information from both GISAID and NCBI. I have parsed this data in R into 4 column region, country, division, and city. However there is a discrepancy between the region in my parsed data and augur. for example, for China the region in my data is “asia” whilst in Augur it should be “china” as a region. Similarly for Japan where the region for augur is should be “japan_korea”.

My question is will Augur handle this correctly based on the correct country name and (backwords?) replace the region with the correct one or do I already need to prepare the correct region? This is not clear from the Preparing Your Metadata — Augur 23.1.1 documentation documentation.

Hope I’ve explained it well but let me know if more clarification is needed.

Best,
Jurre

2

Hi @jurresiegers,

for example, for China the region in my data is “asia” whilst in Augur it should be “china” as a region. Similarly for Japan where the region for augur is should be “japan_korea”.

Based on this statement, I’m guessing you are either referring the colors.tsv or the lat_longs.tsv in Augur.

These are just the default values that come with Augur. If you have regions that differ, you can provide custom colors and/or custom lat longs to Augur.

Best,
Jover