Merge pull request #19 from nextstrain/nextclade-tweaks

Nextclade tweaks

nextclade/defaults/nextclade-dataset/CHANGELOG.md

@@ -1,3 +1,3 @@
 ## Unreleased
 
-Initial release of yellow fever virus dataset.
+Initial release of yellow fever virus (prM-E region only) dataset.

nextclade/defaults/nextclade-dataset/README.md

@@ -1,4 +1,4 @@
-# Yellow fever virus dataset
+# Yellow fever virus (prM-E region only) dataset
 
 | Key               | Value                                                            |
 | ----------------- | -----------------------------------------------------------------|
@@ -36,7 +36,7 @@ following genotypes as described in the aforementioned two papers:
 
 (N.b., the reference sequence used in this data set is actually 672nt
 long, from bases 641-1312 of the genome reference. The 2 extra bases
-make the reference an complete open reading frame.)
+make the reference a complete open reading frame.)
 
 This dataset can be used to assign genotypes to any sequence that
 includes at least 500 bp of the prM-E region, including whole genome

nextclade/defaults/nextclade-dataset/pathogen.json

@@ -15,8 +15,7 @@
   },
   "schemaVersion": "3.0.0",
   "alignmentParams": {
-      "minSeedCover": 0.01,
-      "minLength": 500
+      "minSeedCover": 0.01
   },
   "qc": {
     "missingData": {
@@ -36,8 +35,8 @@
     },
     "privateMutations": {
       "enabled": true,
-      "cutoff": 8,
-      "typical": 2,
+      "cutoff": 12,
+      "typical": 4,
       "weightLabeledSubstitutions": 1,
       "weightReversionSubstitutions": 1,
       "weightUnlabeledSubstitutions": 1