Assignment cache from pango-designation v1.17 on GISAID sequences dow…

[AngieHinrichs]

Assignment cache from pango-designation v1.17 on GISAID sequences downloaded through 2022-12-10

The cache was computed at UCSC on sequences downloaded from GISAID, using pangolin with the --skip-scorpio flag and --usher-tree <v1.17 lineageTree.pb> file prior to v1.17 release.

This time, in order to take advantage of speed improvements as well as improvements in how N bases are handled and multiple equally parsimonious placements are counted in the new usher-sampled program in UShER release 0.6.1, a branch build of pangolin was used instead of the latest pangolin release: https://github.com/AngieHinrichs/pangolin/tree/usher-sampled The branch will hopefully soon be incorporated into pangolin via pull request cov-lineages/pangolin#499 .

pangolin: 4.1.3 *** branch: https://github.com/AngieHinrichs/pangolin/tree/usher-sampled
usher 0.6.1
gofasta 1.1.0
minimap2 2.24-r1122
faToVcf: 426