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loculus-project / loculus

An open-source software package to power microbial genomic databases
https://loculus.org
GNU Affero General Public License v3.0
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Have an explicit sequence length cut-off in preprocessing #2722

Closed anna-parker closed 2 months ago

anna-parker commented 2 months ago

We use nextclade for alignment which has a minimum sequence length (the default is 100bp). We should check if this is the best choice and potentially change our preprocessing configs to reflect this.

anna-parker commented 2 months ago

I see Theo has already opened an issue for this - sorry! https://github.com/loculus-project/loculus/issues/2721

corneliusroemer commented 2 months ago

We possibly want a different cutoff for ingest and for non-ingest sequences

If we lower the cutoff for user submissions, we may want to have to configure and extra filter in ingest.

corneliusroemer commented 2 months ago

Then close as "not planned" = gray not as completed ;)