diff --git a/nextclade/README.md b/nextclade/README.md index 0fe50bf..fbd5ced 100644 --- a/nextclade/README.md +++ b/nextclade/README.md @@ -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 .` diff --git a/nextclade/defaults/clades.tsv b/nextclade/defaults/clades.tsv index 72af86e..39117a7 100644 --- a/nextclade/defaults/clades.tsv +++ b/nextclade/defaults/clades.tsv @@ -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 diff --git a/nextclade/defaults/colors.tsv b/nextclade/defaults/colors.tsv index 75226a7..6b8036c 100644 --- a/nextclade/defaults/colors.tsv +++ b/nextclade/defaults/colors.tsv @@ -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