corneliusroemer
commented
1 year ago These probably are Spike only sequences for which the current dataset used by Nextclade doesn't work reliably either.
Spike only is not assigned by pangolin.
Nextclade has issues as well if the breakpoint is not in Spike.
We'll fix this in Nextclade at some point.
For now the workaround is to use the dedicated sars-cov-2-no-recomb dataset, then things work out for Spike only (common in South Korea and Austria)
On Fri, Oct 21, 2022, 19:59 AnonymousUserUse @.***> wrote:
I wonder how many sequences are classified as "unassigned" by pangoLEARN. That is for the comparison/query between pangoLEARN and Nextclade (e.g. unassigned & nextcladePangoLineage:XAN) meaningful.
Both simple module and advanced query do not work for unassigned:
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?pangoLineage=Unassigned& shows 0 sequence;
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=Unassigned& results error.
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I wonder how many sequences are classified as "unassigned" by pangoLEARN. That is for the comparison/query between pangoLEARN and Nextclade (e.g. unassigned & nextcladePangoLineage:XAN) meaningful.
Both simple module and advanced query do not work for unassigned: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?pangoLineage=Unassigned& shows 0 sequence; https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=Unassigned& results error.