pangolin v3.1.4

Release notes

• Patch to not overwrite lineage if scorpio outputs a call with ambiguous lineage mappings.
• Thanks @ArtPoon for flagging (https://twitter.com/art_poon/status/1406260677392715778)!

pangolin v3.1.3

Minor release:

• Better handles cases where no lineage assignment but there is a scorpio call
• Handles cases where the scorpio constellation name is ambiguous
• Adds to help menu description to clarify that -dv gives the pango-designation trained version, not the most up to date pango-designation version in the environment

pangolin v3.1.2

UShER now resolves lineage calls to one with most placements
(2c7a04d).

pangolin v3.1

Release notes

• FULL ENV UPDATE REQUIRED with this release
• Curated final lineage call, lineage conflicts between scorpio and pangoLEARN/ UShER are resolved by taking the scorpio call. Any changes to the assignment are listed in the notes column (thanks @rmcolq).
• More flexible usher dependency until bioconda release for MacOSX
• UShER handles empty input in snakemake (thanks @AngieHinrichs).

Additional dependencies: pango-designation repository

If you don't wish to do a full env update running:

pip install git+https://github.com/cov-lineages/pango-designation.git

in the pangolin environment will install the additional repo. This provides the alias json file to pangolin directly from pango-designation.

pangolin v3.0.5

Release notes

• sklearn version now flexible with >=0.23.1 in setup.py

pangolin v3.0.4

Release notes

• Extra quotes around args to account for spaces in path names (potential bug fix for using --no-temp arg)
• Extra checks at import to catch if deps aren't installed, tries to import if it can't prints how to install it for scorpio, constellations and pangoLEARN

pangolin v3.0.3

Release notes

• Addition of constellations to --update flag
• Addition of new flag --update-data that only updates pangoLEARN and scorpio, rather than pangolin software
• Fixing bug flagged in issue #206
• Scorpio to run all VOCS and VUIs present in constellations now

pangolin v3.0.2

Release notes

• Patch to call all three VOCs with scorpio.

pangolin v3.0.1

Release notes

• Patch to catch case of pangoLEARN running but all seqs assigned via the hash.

pangolin v3.0

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

• NOTE: Output file columns have changed, details can be found at https://cov-lineages.org/pangolin_docs/output.html.