pangolin-data v1.28.1

Removed annotation of KR.2 which was accidentally included in v1.28 as a child of LT.1 instead of being completely replaced by LT.1, causing most LT.1 sequences to be assigned KR.2. (See #60) No change to alias file, still pango-designation v1.28.

pangolin-data v1.28

Release of pangolin-data repository corresponding to pango-designation version 1.28. This repository is compatible with pangolin v4.3 onwards.

pangolin-data v1.27

Release of pangolin-data repository corresponding to pango-designation version 1.27. This repository is compatible with pangolin v4.3 onwards.

pangolin-data v1.26

Release of pangolin-data repository corresponding to pango-designation version 1.26. This repository is compatible with pangolin v4.3 onwards.

pangolin-data v1.25.1

Minor update: no change to lineageTree.pb; updates to alias_key.json and lineages.hash.csv now use v1.25 pango-designation files as they should (pango-designation v1.24 files were mistakenly used in the pangolin-data v1.25 release).

pangolin-data v1.25

Release of pangolin-data repository corresponding to pango-designation version 1.25. This repository is compatible with pangolin v4.3 onwards.

pangolin-data v1.24

Release of pangolin-data repository corresponding to pango-designation version 1.24. This repository is compatible with pangolin v4.3 onwards.

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.