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pangolin v3.0
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@aineniamh aineniamh released this 27 May 13:25
· 413 commits to master since this release
v3.0
f2f30b0

Release notes: Major release

  • pangolin 3.0 comes with additional functionality and requires an environment update as extra dependencies now include UShER and scorpio.
  • Requires pangoLEARN data >= 2021-05-27

Lineage assignment updates

  • PANGO assignment uses a sequence hash from all currently designated sequences to assign lineages.
  • PLEARN (pangoLEARN) assignment using a machine-learning model to assign the most likely lineage. Current model is decision tree model.
  • PUSHER (pangolin-UShER, pangUSHlin, pangUShER) assignment uses fast parsimony placement of a query sequence into a protobuf file based on currently designated sequences and infers most pasimonious lineage based on this placement (thanks to @AngieHinrichs and the rest of the UShER team).
  • Default --max-ambig value changed to 0.3.

Constellation assignment

  • **NEW FEATURE** pangolin now runs scorpio a tool by @rmcolq and @benjamincjackson to assign the most likely constellation to a given sequence. Full set of possible constellations assigned can be found at: https://github.com/cov-lineages/constellations/tree/main/constellations/definitions
  • This replaces the post-hoc tests pangolin previously ran to curate the variant of concern calls. The output of scorpio, which is explict SNP-threshold based assignment, and pangolin, which can now use either the pangoLEARN or UShER infererence engines, are displayed side-by-side in the output report.

Input updates

  • Based on @ArtPoon's PR, pangolin is now gzip and lzma compatible.

Output updates

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