Updated QC parameters

nextstrain · Aug 13, 2024 · cc5b64b · cc5b64b
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Showing 29 changed files with 26 additions and 16 deletions.
diff --git a/...b/dengue-lineages/all-serotypes/README.md → ...unity/v-gen-lab/dengue-lineages/README.md b/...b/dengue-lineages/all-serotypes/README.md → ...unity/v-gen-lab/dengue-lineages/README.md
@@ -4,6 +4,8 @@ These datasets are based on the dengue virus lineage systems described by [Verit
 
 More information about the Dengue Lineages project: [Dengue Lineages website](https://dengue-lineages.org/), [GitHub Repository](https://github.com/DENV-lineages)
 
+The source code is avalible on [V-GEN-Lab/dengue-lineages-nextclade](https://github.com/V-GEN-Lab/dengue-lineages-nextclade)
+For bugs, please open an [Issue](https://github.com/V-GEN-Lab/dengue-lineages-nextclade/issues)
 
 ## Authors and contacts
 

diff --git a/...lineages/all-serotypes/denv1/CHANGELOG.md → ...en-lab/dengue-lineages/denv1/CHANGELOG.md b/...lineages/all-serotypes/denv1/CHANGELOG.md → ...en-lab/dengue-lineages/denv1/CHANGELOG.md
diff --git a/...ue-lineages/all-serotypes/denv1/README.md → ...v-gen-lab/dengue-lineages/denv1/README.md b/...ue-lineages/all-serotypes/denv1/README.md → ...v-gen-lab/dengue-lineages/denv1/README.md
@@ -15,6 +15,8 @@ This dataset is based on the dengue virus lineage system from [Verity et al., 20
 ## Authors and contacts
 
 Maintainers: [James Siqueira Pereira](https://github.com/jamessiqueirap) and [Alex Ranieri](https://github.com/alex-ranieri).
+The source code is avalible on [V-GEN-Lab/dengue-lineages-nextclade](https://github.com/V-GEN-Lab/dengue-lineages-nextclade)
+For bugs, please open an [Issue](https://github.com/V-GEN-Lab/dengue-lineages-nextclade/issues)
 
 ## Dengue Lineages System Project
 

diff --git a/...ll-serotypes/denv1/genome_annotation.gff3 → ...gue-lineages/denv1/genome_annotation.gff3 b/...ll-serotypes/denv1/genome_annotation.gff3 → ...gue-lineages/denv1/genome_annotation.gff3
diff --git a/...ineages/all-serotypes/denv1/pathogen.json → ...n-lab/dengue-lineages/denv1/pathogen.json b/...ineages/all-serotypes/denv1/pathogen.json → ...n-lab/dengue-lineages/denv1/pathogen.json
@@ -33,8 +33,8 @@
     "treeJson": "tree.json"
   },
   "meta": {
-    "bugs": "https://github.com/DENV-lineages/nextclade_data/issues",
-    "source code": "https://github.com/DENV-lineages/nextclade_data"
+    "bugs": "https://github.com/V-GEN-Lab/dengue-lineages-nextclade/issues",
+    "source code": "https://github.com/V-GEN-Lab/dengue-lineages-nextclade"
   },
   "qc": {
     "frameShifts": {
@@ -50,9 +50,9 @@
       "mixedSitesThreshold": 8
     },
     "privateMutations": {
-      "cutoff": 25,
+      "cutoff": 168,
       "enabled": true,
-      "typical": 15,
+      "typical": 56,
       "weightLabeledSubstitutions": 2,
       "weightReversionSubstitutions": 1,
       "weightUnlabeledSubstitutions": 1

diff --git a/...eages/all-serotypes/denv1/reference.fasta → ...lab/dengue-lineages/denv1/reference.fasta b/...eages/all-serotypes/denv1/reference.fasta → ...lab/dengue-lineages/denv1/reference.fasta
diff --git a/...eages/all-serotypes/denv1/sequences.fasta → ...lab/dengue-lineages/denv1/sequences.fasta b/...eages/all-serotypes/denv1/sequences.fasta → ...lab/dengue-lineages/denv1/sequences.fasta
diff --git a/...ue-lineages/all-serotypes/denv1/tree.json → ...v-gen-lab/dengue-lineages/denv1/tree.json b/...ue-lineages/all-serotypes/denv1/tree.json → ...v-gen-lab/dengue-lineages/denv1/tree.json
diff --git a/...lineages/all-serotypes/denv2/CHANGELOG.md → ...en-lab/dengue-lineages/denv2/CHANGELOG.md b/...lineages/all-serotypes/denv2/CHANGELOG.md → ...en-lab/dengue-lineages/denv2/CHANGELOG.md
diff --git a/...ue-lineages/all-serotypes/denv2/README.md → ...v-gen-lab/dengue-lineages/denv2/README.md b/...ue-lineages/all-serotypes/denv2/README.md → ...v-gen-lab/dengue-lineages/denv2/README.md
@@ -15,6 +15,8 @@ This dataset is based on the dengue virus lineage system from [Verity et al., 20
 ## Authors and contacts
 
 Maintainers: [James Siqueira Pereira](https://github.com/jamessiqueirap) and [Alex Ranieri](https://github.com/alex-ranieri).
+The source code is avalible on [V-GEN-Lab/dengue-lineages-nextclade](https://github.com/V-GEN-Lab/dengue-lineages-nextclade)
+For bugs, please open an [Issue](https://github.com/V-GEN-Lab/dengue-lineages-nextclade/issues)
 
 ## Dengue Lineages System Project
 

diff --git a/...ll-serotypes/denv2/genome_annotation.gff3 → ...gue-lineages/denv2/genome_annotation.gff3 b/...ll-serotypes/denv2/genome_annotation.gff3 → ...gue-lineages/denv2/genome_annotation.gff3
diff --git a/...ineages/all-serotypes/denv2/pathogen.json → ...n-lab/dengue-lineages/denv2/pathogen.json b/...ineages/all-serotypes/denv2/pathogen.json → ...n-lab/dengue-lineages/denv2/pathogen.json
@@ -33,8 +33,8 @@
     "treeJson": "tree.json"
   },
   "meta": {
-    "bugs": "https://github.com/DENV-lineages/nextclade_data/issues",
-    "source code": "https://github.com/DENV-lineages/nextclade_data"
+    "bugs": "https://github.com/V-GEN-Lab/dengue-lineages-nextclade/issues",
+    "source code": "https://github.com/V-GEN-Lab/dengue-lineages-nextclade"
   },
   "qc": {
     "frameShifts": {
@@ -50,9 +50,9 @@
       "mixedSitesThreshold": 8
     },
     "privateMutations": {
-      "cutoff": 25,
+      "cutoff": 216,
       "enabled": true,
-      "typical": 15,
+      "typical": 72,
       "weightLabeledSubstitutions": 2,
       "weightReversionSubstitutions": 1,
       "weightUnlabeledSubstitutions": 1

diff --git a/...eages/all-serotypes/denv2/reference.fasta → ...lab/dengue-lineages/denv2/reference.fasta b/...eages/all-serotypes/denv2/reference.fasta → ...lab/dengue-lineages/denv2/reference.fasta
diff --git a/...eages/all-serotypes/denv2/sequences.fasta → ...lab/dengue-lineages/denv2/sequences.fasta b/...eages/all-serotypes/denv2/sequences.fasta → ...lab/dengue-lineages/denv2/sequences.fasta
diff --git a/...ue-lineages/all-serotypes/denv2/tree.json → ...v-gen-lab/dengue-lineages/denv2/tree.json b/...ue-lineages/all-serotypes/denv2/tree.json → ...v-gen-lab/dengue-lineages/denv2/tree.json
diff --git a/...lineages/all-serotypes/denv3/CHANGELOG.md → ...en-lab/dengue-lineages/denv3/CHANGELOG.md b/...lineages/all-serotypes/denv3/CHANGELOG.md → ...en-lab/dengue-lineages/denv3/CHANGELOG.md
diff --git a/...ue-lineages/all-serotypes/denv3/README.md → ...v-gen-lab/dengue-lineages/denv3/README.md b/...ue-lineages/all-serotypes/denv3/README.md → ...v-gen-lab/dengue-lineages/denv3/README.md
@@ -15,6 +15,8 @@ This dataset is based on the dengue virus lineage system from [Verity et al., 20
 ## Authors and contacts
 
 Maintainers: [James Siqueira Pereira](https://github.com/jamessiqueirap) and [Alex Ranieri](https://github.com/alex-ranieri).
+The source code is avalible on [V-GEN-Lab/dengue-lineages-nextclade](https://github.com/V-GEN-Lab/dengue-lineages-nextclade)
+For bugs, please open an [Issue](https://github.com/V-GEN-Lab/dengue-lineages-nextclade/issues)
 
 ## Dengue Lineages System Project
 

diff --git a/...ll-serotypes/denv3/genome_annotation.gff3 → ...gue-lineages/denv3/genome_annotation.gff3 b/...ll-serotypes/denv3/genome_annotation.gff3 → ...gue-lineages/denv3/genome_annotation.gff3
diff --git a/...ineages/all-serotypes/denv3/pathogen.json → ...n-lab/dengue-lineages/denv3/pathogen.json b/...ineages/all-serotypes/denv3/pathogen.json → ...n-lab/dengue-lineages/denv3/pathogen.json
@@ -33,8 +33,8 @@
     "treeJson": "tree.json"
   },
   "meta": {
-    "bugs": "https://github.com/DENV-lineages/nextclade_data/issues",
-    "source code": "https://github.com/DENV-lineages/nextclade_data"
+    "bugs": "https://github.com/V-GEN-Lab/dengue-lineages-nextclade/issues",
+    "source code": "https://github.com/V-GEN-Lab/dengue-lineages-nextclade"
   },
   "qc": {
     "frameShifts": {
@@ -50,9 +50,9 @@
       "mixedSitesThreshold": 8
     },
     "privateMutations": {
-      "cutoff": 25,
+      "cutoff": 210,
       "enabled": true,
-      "typical": 15,
+      "typical": 70,
       "weightLabeledSubstitutions": 2,
       "weightReversionSubstitutions": 1,
       "weightUnlabeledSubstitutions": 1

diff --git a/...eages/all-serotypes/denv3/reference.fasta → ...lab/dengue-lineages/denv3/reference.fasta b/...eages/all-serotypes/denv3/reference.fasta → ...lab/dengue-lineages/denv3/reference.fasta
diff --git a/...eages/all-serotypes/denv3/sequences.fasta → ...lab/dengue-lineages/denv3/sequences.fasta b/...eages/all-serotypes/denv3/sequences.fasta → ...lab/dengue-lineages/denv3/sequences.fasta
diff --git a/...ue-lineages/all-serotypes/denv3/tree.json → ...v-gen-lab/dengue-lineages/denv3/tree.json b/...ue-lineages/all-serotypes/denv3/tree.json → ...v-gen-lab/dengue-lineages/denv3/tree.json
diff --git a/...lineages/all-serotypes/denv4/CHANGELOG.md → ...en-lab/dengue-lineages/denv4/CHANGELOG.md b/...lineages/all-serotypes/denv4/CHANGELOG.md → ...en-lab/dengue-lineages/denv4/CHANGELOG.md
diff --git a/...ue-lineages/all-serotypes/denv4/README.md → ...v-gen-lab/dengue-lineages/denv4/README.md b/...ue-lineages/all-serotypes/denv4/README.md → ...v-gen-lab/dengue-lineages/denv4/README.md
@@ -15,6 +15,8 @@ This dataset is based on the dengue virus lineage system from [Verity et al., 20
 ## Authors and contacts
 
 Maintainers: [James Siqueira Pereira](https://github.com/jamessiqueirap) and [Alex Ranieri](https://github.com/alex-ranieri).
+The source code is avalible on [V-GEN-Lab/dengue-lineages-nextclade](https://github.com/V-GEN-Lab/dengue-lineages-nextclade)
+For bugs, please open an [Issue](https://github.com/V-GEN-Lab/dengue-lineages-nextclade/issues)
 
 ## Dengue Lineages System Project
 

diff --git a/...ll-serotypes/denv4/genome_annotation.gff3 → ...gue-lineages/denv4/genome_annotation.gff3 b/...ll-serotypes/denv4/genome_annotation.gff3 → ...gue-lineages/denv4/genome_annotation.gff3
diff --git a/...ineages/all-serotypes/denv4/pathogen.json → ...n-lab/dengue-lineages/denv4/pathogen.json b/...ineages/all-serotypes/denv4/pathogen.json → ...n-lab/dengue-lineages/denv4/pathogen.json
@@ -33,8 +33,8 @@
     "treeJson": "tree.json"
   },
   "meta": {
-    "bugs": "https://github.com/DENV-lineages/nextclade_data/issues",
-    "source code": "https://github.com/DENV-lineages/nextclade_data"
+    "bugs": "https://github.com/V-GEN-Lab/dengue-lineages-nextclade/issues",
+    "source code": "https://github.com/V-GEN-Lab/dengue-lineages-nextclade"
   },
   "qc": {
     "frameShifts": {
@@ -50,9 +50,9 @@
       "mixedSitesThreshold": 8
     },
     "privateMutations": {
-      "cutoff": 25,
+      "cutoff": 276,
       "enabled": true,
-      "typical": 15,
+      "typical": 92,
       "weightLabeledSubstitutions": 2,
       "weightReversionSubstitutions": 1,
       "weightUnlabeledSubstitutions": 1

diff --git a/...eages/all-serotypes/denv4/reference.fasta → ...lab/dengue-lineages/denv4/reference.fasta b/...eages/all-serotypes/denv4/reference.fasta → ...lab/dengue-lineages/denv4/reference.fasta
diff --git a/...eages/all-serotypes/denv4/sequences.fasta → ...lab/dengue-lineages/denv4/sequences.fasta b/...eages/all-serotypes/denv4/sequences.fasta → ...lab/dengue-lineages/denv4/sequences.fasta
diff --git a/...ue-lineages/all-serotypes/denv4/tree.json → ...v-gen-lab/dengue-lineages/denv4/tree.json b/...ue-lineages/all-serotypes/denv4/tree.json → ...v-gen-lab/dengue-lineages/denv4/tree.json