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Nextclade tweaks #19

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merged 2 commits into from
Oct 17, 2024
Merged

Nextclade tweaks #19

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9e19e2c
Update nextclade files based on PR feedback
genehack Oct 17, 2024
2e33696
Add some Clade III example sequences
genehack Oct 17, 2024
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2 changes: 1 addition & 1 deletion nextclade/defaults/nextclade-dataset/CHANGELOG.md
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## Unreleased

Initial release of yellow fever virus dataset.
Initial release of yellow fever virus (prM-E region only) dataset.
4 changes: 2 additions & 2 deletions nextclade/defaults/nextclade-dataset/README.md
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# Yellow fever virus dataset
# Yellow fever virus (prM-E region only) dataset

| Key | Value |
| ----------------- | -----------------------------------------------------------------|
Expand Down Expand Up @@ -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
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7 changes: 3 additions & 4 deletions nextclade/defaults/nextclade-dataset/pathogen.json
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Expand Up @@ -15,8 +15,7 @@
},
"schemaVersion": "3.0.0",
"alignmentParams": {
"minSeedCover": 0.01,
"minLength": 500
"minSeedCover": 0.01
},
"qc": {
"missingData": {
Expand All @@ -36,8 +35,8 @@
},
"privateMutations": {
"enabled": true,
"cutoff": 8,
"typical": 2,
"cutoff": 12,
"typical": 4,
"weightLabeledSubstitutions": 1,
"weightReversionSubstitutions": 1,
"weightUnlabeledSubstitutions": 1
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