Add QC parameters to pathogen.json

nextstrain · May 7, 2024 · 503df23 · 503df23
1 parent 751cb5c
commit 503df23
Showing 1 changed file with 25 additions and 5 deletions.
diff --git a/nextclade_dataset/pathogen.json b/nextclade_dataset/pathogen.json
@@ -6,10 +6,30 @@
 	  "treeJson": "measles_nextclade.json"
 	},
 	"attributes": {
-	  "name": "Measles"
+	  "name": "Measles (N450)",
+	  "reference name": "Ichinose-B95a",
+      "reference accession": "NC_001498.1"
 	},
-	"schemaVersion": "3.0.0",
-	"version": {
-	  "tag": "unreleased"
-	}
+	"schemaVersion": "1.0.0",
+	"alignmentParams": {
+		"minSeedCover": 0.01,
+		"minLength": 400
+	  },
+    "qc": {
+		"missingData": {
+		  "enabled": true,
+		  "missingDataThreshold": 20,
+		  "scoreBias": 4
+		},
+		"mixedSites": {
+		  "enabled": true,
+		  "mixedSitesThreshold": 4
+		},
+		"frameShifts": {
+		  "enabled": true
+		},
+		"stopCodons": {
+		  "enabled": true
+		}
+	  }
   }