Skip to content

Commit

Permalink
Relabel clades numerically, rather than geographically [#12]
Browse files Browse the repository at this point in the history
Also update nextclade build README to give mapping back to literature
genotypes.
genehack committed Aug 20, 2024
1 parent 1c8192b commit f75390b
Showing 3 changed files with 60 additions and 47 deletions.
15 changes: 14 additions & 1 deletion nextclade/README.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# Yellow Fever Virus Nextclade Dataset Tree

This workflow creates a phylogenetic tree that can be used as part of
a Nextclade dataset to assign genotypes to yellow fever virus samples
a Nextclade dataset to assign clades to yellow fever virus samples
based on [Mutebi et al.][] (J Virol. 2001 Aug;75(15):6999-7008) and
[Bryant et al.][] (PLoS Pathog. 2007 May 18;3(5):e75).

@@ -14,6 +14,19 @@ based on [Mutebi et al.][] (J Virol. 2001 Aug;75(15):6999-7008) and
* Provide the following coloring options on the tree:
* Genotype assignment from `augur clades`

The clades we annotate (Clade I-VII) are roughly equivalent with the
following genotypes as described in the aforementioned two papers:

| Clade | Genotype |
|-----------|---------------------|
| Clade I | Angola |
| Clade II | East Africa |
| Clade III | East Central/Africa |
| Clade IV | West Africa I |
| Clade V | West Africa II |
| Clade VI | South America I |
| Clade VII | South America II |

## How to create a new tree

* Run the workflow: `nextstrain build .`
78 changes: 39 additions & 39 deletions nextclade/defaults/clades.tsv
Original file line number Diff line number Diff line change
@@ -1,40 +1,40 @@
clade gene site alt
Angola nuc 111 G
Angola nuc 219 T
Angola nuc 240 C
Angola nuc 246 A
Angola nuc 252 A
Angola nuc 255 A
Angola nuc 291 G
Angola nuc 294 A
Angola nuc 300 A
Angola nuc 315 G
Angola nuc 327 G
Angola nuc 372 A
Angola nuc 420 A
Angola nuc 432 A
Angola nuc 453 T
Angola nuc 492 G
Angola nuc 651 T
Angola nuc 72 A
Angola nuc 81 G
Angola nuc 88 C
Angola nuc 90 A
Angola nuc 99 T
East Africa nuc 171 G
East Africa nuc 438 G
East Africa nuc 45 A
East Africa nuc 468 T
East/Central Africa nuc 228 G
South America I nuc 219 A
South America I nuc 532 A
South America II nuc 114 C
South America II nuc 193 T
South America II nuc 249 A
South America II nuc 639 G
West Africa I nuc 183 G
West Africa I nuc 255 C
West Africa II nuc 270 A
West Africa II nuc 321 T
West Africa II nuc 477 A
West Africa II nuc 93 T
Clade I nuc 111 G
Clade I nuc 219 T
Clade I nuc 240 C
Clade I nuc 246 A
Clade I nuc 252 A
Clade I nuc 255 A
Clade I nuc 291 G
Clade I nuc 294 A
Clade I nuc 300 A
Clade I nuc 315 G
Clade I nuc 327 G
Clade I nuc 372 A
Clade I nuc 420 A
Clade I nuc 432 A
Clade I nuc 453 T
Clade I nuc 492 G
Clade I nuc 651 T
Clade I nuc 72 A
Clade I nuc 81 G
Clade I nuc 88 C
Clade I nuc 90 A
Clade I nuc 99 T
Clade II nuc 171 G
Clade II nuc 438 G
Clade II nuc 45 A
Clade II nuc 468 T
Clade III nuc 228 G
Clade VI nuc 219 A
Clade VI nuc 532 A
Clade VII nuc 114 C
Clade VII nuc 193 T
Clade VII nuc 249 A
Clade VII nuc 639 G
Clade IV nuc 183 G
Clade IV nuc 255 C
Clade V nuc 270 A
Clade V nuc 321 T
Clade V nuc 477 A
Clade V nuc 93 T
14 changes: 7 additions & 7 deletions nextclade/defaults/colors.tsv
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
# genotypes assigned by augur clades
clade_membership Angola #3F63CF
clade_membership East Africa #529AB6
clade_membership East/Central Africa #75B681
clade_membership South America I #A6BE55
clade_membership South America II #D4B13F
clade_membership West Africa I #E68133
clade_membership West Africa II #DC2F24
clade_membership Clade I #3F63CF
clade_membership Clade II #529AB6
clade_membership Clade III #75B681
clade_membership Clade IV #A6BE55
clade_membership Clade V #DC2F24
clade_membership Clade VI #E68133
clade_membership Clade VII #D4B13F

0 comments on commit f75390b

Please sign in to comment.