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reichlab / cladetime

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https://cladetime.readthedocs.io
MIT License
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use root sequence obtained via nextstrain #4

Closed bsweger closed 2 months ago

bsweger commented 5 months ago

In reichlab/variant-nowcast-hub#1, we started pulling reference tree information from the nextstrain API.

Beginning recently, that API call also returns the root sequence, which would be handy to grab, since that's an input to the clade assignment process.

However, the reference tree information being returned isn't in the correct format, so if we want to use it, we'll need to massage the data a bit.

Alternately, if we know for sure that the root sequence doesn't change over time, we could close this issue and just keep using the one we downloaded from NCBI.

bsweger commented 3 months ago

reichlab/variant-nowcast-hub#17 addressed some of this

However, keeping the issue open because I think we can streamline things even more by using a more recent version of the Nextclade CLI.

bsweger commented 2 months ago

Closing, since this task is wrapped into #8.