diff --git a/nextclade/README.md b/nextclade/README.md index ffdb836..6460aa6 100644 --- a/nextclade/README.md +++ b/nextclade/README.md @@ -24,6 +24,7 @@ nextstrain view auspice/ - [ ] Update each `config/{build}/clades.tsv` with new clades - [ ] Add new clades to color ordering +- [ ] Add representative sequences to `resources/include_accessions.txt` - [ ] Check that clades look good, exclude problematic sequences as necessary ### Creating a new dataset version diff --git a/nextclade/resources/all-clades/clades.tsv b/nextclade/resources/all-clades/clades.tsv index 115e0e0..c331b49 100644 --- a/nextclade/resources/all-clades/clades.tsv +++ b/nextclade/resources/all-clades/clades.tsv @@ -63,6 +63,10 @@ C.1 nuc 55133 A C.1 nuc 64426 T C.1 nuc 105923 A +C.1.1 clade C.1 +C.1.1 nuc 21062 T +C.1.1 nuc 149963 T + B.1.4 clade B.1 B.1.4 nuc 34308 A @@ -124,4 +128,12 @@ B.1.19 nuc 148268 T B.1.20 clade B.1 B.1.20 nuc 53326 A B.1.20 nuc 164385 T -B.1.20 nuc 187620 T \ No newline at end of file +B.1.20 nuc 187620 T + +B.1.21 clade B.1 +B.1.21 nuc 22415 A +B.1.21 nuc 132698 T + +B.1.22 clade B.1 +B.1.22 nuc 34784 T +B.1.22 nuc 101418 T diff --git a/nextclade/resources/clade-iib/clades.tsv b/nextclade/resources/clade-iib/clades.tsv index 0c33072..0f02c15 100644 --- a/nextclade/resources/clade-iib/clades.tsv +++ b/nextclade/resources/clade-iib/clades.tsv @@ -64,6 +64,10 @@ C.1 nuc 55133 A C.1 nuc 64426 T C.1 nuc 105923 A +C.1.1 clade C.1 +C.1.1 nuc 21062 T +C.1.1 nuc 149963 T + B.1.4 clade B.1 B.1.4 nuc 34308 A @@ -125,4 +129,12 @@ B.1.19 nuc 148268 T B.1.20 clade B.1 B.1.20 nuc 53326 A B.1.20 nuc 164385 T -B.1.20 nuc 187620 T \ No newline at end of file +B.1.20 nuc 187620 T + +B.1.21 clade B.1 +B.1.21 nuc 22415 A +B.1.21 nuc 132698 T + +B.1.22 clade B.1 +B.1.22 nuc 34784 T +B.1.22 nuc 101418 T diff --git a/nextclade/resources/color_ordering.tsv b/nextclade/resources/color_ordering.tsv index 465c058..758eed3 100644 --- a/nextclade/resources/color_ordering.tsv +++ b/nextclade/resources/color_ordering.tsv @@ -236,6 +236,7 @@ lineage B.1.1 lineage B.1.2 lineage B.1.3 lineage C.1 +lineage C.1.1 lineage B.1.4 lineage B.1.5 lineage B.1.6 @@ -253,6 +254,8 @@ lineage B.1.17 lineage B.1.18 lineage B.1.19 lineage B.1.20 +lineage B.1.21 +lineage B.1.22 lineage A.2 lineage A.2.1 lineage A.2.2 diff --git a/nextclade/resources/include_accessions.txt b/nextclade/resources/include_accessions.txt index 691fc3c..fa4165b 100644 --- a/nextclade/resources/include_accessions.txt +++ b/nextclade/resources/include_accessions.txt @@ -1,5 +1,4 @@ ON563414 #prototypical B.1 -LC753968 #reference for C.1 ON563414 #reference for B.1 ON843175 #reference for B.1.9 OP215224 #reference for B.1.8 @@ -15,7 +14,7 @@ ON929079 #reference for B.1.2 OP442552 #reference for B.1.17 ON694335 #reference for B.1.15 OP693647 #reference for B.1.16 -OP642395 #reference for B.1.16 +OP642395 #reference for B.1.16 ON694342 #reference for B.1.14 OP838893 #reference for B.1.19 OP169336 #reference for B.1.11 @@ -26,3 +25,9 @@ OP536663 #reference for B.1.13 OP257254 #reference for B.1.13 OP205110 #reference for B.1.10 OQ320441 #reference for B.1.20 +OP539939 #reference for B.1.21 +OQ773522 #reference for B.1.22 +OR095023 #reference for B.1.22 +LC753968 #reference for C.1 +LC753968 #reference for C.1.1 +OR643705 #reference for C.1.1 diff --git a/nextclade/resources/lineage-b.1/clades.tsv b/nextclade/resources/lineage-b.1/clades.tsv index e0305f4..505aac9 100644 --- a/nextclade/resources/lineage-b.1/clades.tsv +++ b/nextclade/resources/lineage-b.1/clades.tsv @@ -24,6 +24,10 @@ C.1 nuc 55133 A C.1 nuc 64426 T C.1 nuc 105923 A +C.1.1 clade C.1 +C.1.1 nuc 21062 T +C.1.1 nuc 149963 T + B.1.4 clade B.1 B.1.4 nuc 34308 A @@ -85,4 +89,12 @@ B.1.19 nuc 148268 T B.1.20 clade B.1 B.1.20 nuc 53326 A B.1.20 nuc 164385 T -B.1.20 nuc 187620 T \ No newline at end of file +B.1.20 nuc 187620 T + +B.1.21 clade B.1 +B.1.21 nuc 22415 A +B.1.21 nuc 132698 T + +B.1.22 clade B.1 +B.1.22 nuc 34784 T +B.1.22 nuc 101418 T