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robert-koch-institut / SARS-CoV-2-Sequenzdaten_aus_Deutschland

Ein zentraler Bestandteil einer erfolgreichen Erregersurveillance ist das Verständnis der Verbreitung eines Erregers sowie seiner pathogenen Eigenschaften. Hierbei stellt das Wissen über das Erregergenom eine wichtige Informationsquelle dar. So erlaubt der Nachweis von Mutationen im Genom eines Erregers, Verwandtschaftsbeziehungen zu rekonstruie...
https://robert-koch-institut.github.io/SARS-CoV-2-Sequenzdaten_aus_Deutschland/
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documentation of PROCESSING_DATE missing in readme #5

Closed rgerhards closed 2 years ago

rgerhards commented 2 years ago

The CSV field PROCESSING_DATE is not documented. I assume it is the lab sequencing date?

cuehs commented 2 years ago

PROCESSING_DATE is an internal field, I am not sure why it is in the public repository. regardless: RECEIVE_DATE and PROCESSING_DATE both indicate when the sequence was uploaded to the RKI and when it was processed at RKI (usually that's the same day)

I just saw the twitter conversation: DATE_DRAW can be used as a proxy of when an infection occurred. PRIMEDIAGNOSTIC_LAB_PC can be used as a proxy for the location of the infection.

Unfortunately the number of sequences becomes only really informative after 10 days or so (the average delay between the date the "schnelltest" sample is taken and the pcr result is uploaded to us).

cuehs commented 2 years ago

fixed by #12