pangolin-assignment v1.28.1

Assignment cache from pango-designation v1.28 on GISAID sequences downloaded through 2024-07-01, rebuilt for pangolin-data and pangolin-assignment release v1.28.1 (minor release to fix accidental inclusion of KR.2, see cov-lineages/pangolin-data#60).

The cache was computed at UCSC on sequences downloaded from GISAID, using pangolin with the --skip-scorpio flag and --usher-tree <v1.28.1 lineageTree.pb> file prior to v1.28.1 release.

pangolin: 4.3.1
usher 0.6.3
gofasta 1.2.1
minimap2 2.26-r1175
faToVcf: 448

pangolin-assignment v1.28

Assignment cache from pango-designation v1.28 on GISAID sequences downloaded through 2024-06-21

The cache was computed at UCSC on sequences downloaded from GISAID, using pangolin with the --skip-scorpio flag and --usher-tree <v1.28 lineageTree.pb> file prior to v1.28 release.

pangolin: 4.3.1
usher 0.6.3
gofasta 1.2.1
minimap2 2.26-r1175
faToVcf: 448

pangolin-assignment v1.27

Assignment cache from pango-designation v1.27 on GISAID sequences downloaded through 2024-04-24

The cache was computed at UCSC on sequences downloaded from GISAID, using pangolin with the --skip-scorpio flag and --usher-tree <v1.27 lineageTree.pb> file prior to v1.27 release.

pangolin: 4.3.1
usher 0.6.3
gofasta 1.2.1
minimap2 2.26-r1175
faToVcf: 448

pangolin-assignment v1.26

Assignment cache from pango-designation v1.26 on GISAID sequences downloaded through 2024-03-08

The cache was computed at UCSC on sequences downloaded from GISAID, using pangolin with the --skip-scorpio flag and --usher-tree <v1.26 lineageTree.pb> file prior to v1.26 release.

pangolin: 4.3.1
usher 0.6.3
gofasta 1.2.1
minimap2 2.26-r1175
faToVcf: 448

pangolin-assignment v1.25.1

Assignment cache from pango-designation v1.25 on GISAID sequences downloaded through 2024-02-09, rebuilt for pangolin-data and pangolin-assignment release v1.25.1. [No change to assignments, just re-gzipped; bumping version to stay in sync with pangolin-data.]

pangolin-assignment v1.25

Assignment cache from pango-designation v1.25 on GISAID sequences downloaded through 2024-02-09

The cache was computed at UCSC on sequences downloaded from GISAID, using pangolin with the --skip-scorpio flag and --usher-tree <v1.25 lineageTree.pb> file prior to v1.25 release.

pangolin: 4.3.1
usher 0.6.3
gofasta 1.2.1
minimap2 2.26-r1175
faToVcf: 448

pangolin-assignment v1.24

Assignment cache from pango-designation v1.24 on GISAID sequences downloaded through 2024-01-19

The cache was computed at UCSC on sequences downloaded from GISAID, using pangolin with the --skip-scorpio flag and --usher-tree <v1.24 lineageTree.pb> file prior to v1.24 release.

pangolin: 4.3.1
usher 0.6.3
gofasta 1.2.0
minimap2 2.24-r1122
faToVcf: 448

pangolin-assignment v1.23.1

pangolin-data v1.23.1 minor release adds JQ to alias_key.json, which has no effect on the cached lineage assignments; pangolin-data's alias_key.json is used only for comparison of inference lineage (from usher) with scorpio assignment.

pangolin-assignment v1.23

Assignment cache from pango-designation v1.23 on GISAID sequences downloaded through 2023-10-16

The cache was computed at UCSC on sequences downloaded from GISAID, using pangolin with the --skip-scorpio flag and --usher-tree <v1.23 lineageTree.pb> file prior to v1.23 release.

*** NOTE: for v1.23 only, a modified version of usher was used; this modified version is expected to become usher version 0.6.3. It has a bugfix for a corner case that causes some lineage A samples to be assigned to A.* sublineages or even B or B.* sublineages. The v1.23 tree triggers the bug in more cases than the previous trees which is why the bug was not discovered until this release.

If you will be running pangolin on early 2020 sequences that may be lineage A, it is highly recommended to use the assignment cache and to update usher to 0.6.3 as soon as it is released.

pangolin: 4.3.1
usher 0.6.3 (not yet released)
gofasta 1.2.0
minimap2 2.24-r1122
faToVcf: 426

pangolin-assignment v1.22

Assignment cache from pango-designation v1.22 on GISAID sequences downloaded through 2023-08-17

The cache was computed at UCSC on sequences downloaded from GISAID, using pangolin with the --skip-scorpio flag and --usher-tree <v1.22 lineageTree.pb> file prior to v1.22 release.

pangolin: 4.3.1
usher 0.6.2
gofasta 1.2.0
minimap2 2.24-r1122
faToVcf: 426