pangolin-data v1.23.1

The lineageTree.pb for pangolin-data v1.23 accidentally included several lineages that were designated just after pango-designation release v1.23: BA.2.86.2, BA.2.86.3 and JQ.1. The pangolin-data v1.23 file alias_key.json, a copy of pango-designation's v1.23 alias_key.json, did not include the alias JQ. That discrepancy causes errors when JQ.1 is assigned by UShER and pangolin is not run with the --skip-scorpio flag, because the comparison between UShER-assigned lineage JQ.1 and scorpio VoC call requires lookup of the JQ alias.

Instead of removing BA.2.86.2, BA.2.86.3 and JQ.1 from lineageTree.pb, this minor release adds JQ to pangolin-data's alias_key.json to avoid errors when JQ.1 is assigned.

pangolin-data v1.23

Release of pangolin-data repository corresponding to pango-designation version 1.23. This repository is compatible with pangolin v4.3 onwards.

*** NOTE: the v1.23 tree provokes a corner-case bug in usher-sampled prior to version 0.6.3 that causes some lineage A samples to be assigned to A.* sublineages or even B or B.* sublineages. If you will be running pangolin on early 2020 sequences that may be lineage A, then it is highly recommended to use the assignment cache (install by running pangolin --add-assignment-cache, run pangolin on input sequences with --use-assignment-cache) and to update the usher package in your pangolin environment to 0.6.3 as soon as it is released.

pangolin-data v1.22

Release of pangolin-data repository corresponding to pango-designation version 1.22. This repository is compatible with pangolin v4.3 onwards.

pangolin-data v1.21

Release of pangolin-data repository corresponding to pango-designation version 1.21. This repository is compatible with pangolin v4.3 onwards.

pangolin-data v1.20

Release of pangolin-data repository corresponding to pango-designation version 1.20. This repository is compatible with pangolin v4.3 onwards.

Due to lack of resources the pangoLEARN model files will not be updated going forward (and have not been updated since pangolin-data release v1.18). As of release v1.20, the files have been removed from this repository. pangolin v4.3 does not expect pangolin-data to include the files, and will not run --analysis-mode pangolearn unless --datadir is also provided specifying a directory that contains pangoLEARN model files.

pangolin-data v1.19

Release of pangolin-data repository corresponding to pango-designation version 1.19. This repository is compatible with pangolin v4.0 onwards.

Only the UShER tree is being updated, not the pangoLEARN model, due to issues with the server used for training the model.

pangolin-data v1.18.1.1

https://github.com/cov-lineages/pangolin-data/releases/tag/v1.18.1 included an update to lineageTree.pb but was missing the corresponding update to alias_key.json and lineages.hash.csv (#35). This minor release updates those files (no change to lineageTree.pb).

pangolin-data v1.18.1

Release of pangolin-data repository corresponding to pango-designation version 1.18.1. This repository is compatible with pangolin v4.0 onwards.

This is a minor release (v1.18.1 instead of v1.19) because only the UShER tree is being updated, not the pangoLEARN model, due to issues with the server used for training the model.

pangolin-data v1.18

Release of pangolin-data repository corresponding to pango-designation version 1.18. This repository is compatible with pangolin v4.0 onwards.

pangolin-data v1.17

Release of pangolin-data repository corresponding to pango-designation version 1.17. This repository is compatible with pangolin v4.0 onwards.