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Only include more recent context sequences
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For when subsampling in the Nextstrain GISAID profile, rather than treating early contextual samples as origin of pandemic to beginning of focal window, eg for 6m analysis from 2020 to 6m ago, instead use a consistent 24m of additional context. So, for 6m, this is context of 30m ago to 6m and focal of 6m ago to present. Additionally, reduce the amount of contextual sequences included from a 4:1 ratio of focal to context to a 10:1 ratio of focal to context.
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trvrb committed Jul 24, 2024
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