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Trying out a reference-only dataset #124

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bdae2aa
Trying out a reference-only dataset
corneliusroemer Dec 20, 2023
5030543
Add +1 in minimizer normalization to avoid divide by 0
corneliusroemer Dec 20, 2023
c624996
chore: rebuild [skip ci]
nextstrain-bot Dec 20, 2023
6974eec
Add example sequences
corneliusroemer Dec 20, 2023
6c27d08
chore: rebuild [skip ci]
nextstrain-bot Dec 20, 2023
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3 changes: 2 additions & 1 deletion data/nextstrain/collection.json
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"nextstrain/flu/h3n2/pa",
"nextstrain/flu/h1n1pdm/pb2",
"nextstrain/flu/h1n1pdm/pb1",
"nextstrain/flu/h3n2/pb2"
"nextstrain/flu/h3n2/pb2",
"nextstrain/scratch/reference-only"
]
}
5 changes: 5 additions & 0 deletions data/nextstrain/scratch/reference-only/CHANGELOG.md
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## Unreleased

Initial release of this v3 dataset.

This dataset is new to v3 and does not have a v2 equivalent.
7 changes: 7 additions & 0 deletions data/nextstrain/scratch/reference-only/README.md
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# Scratch dataset for alignment to custom reference

## Scope of this dataset

This dataset is a minimal example to allow users to upload their own reference sequence and align some other sequences to that reference.

To use this dataset, you _must_ upload your own reference sequence in FASTA format, through the "customize" interface.
4 changes: 4 additions & 0 deletions data/nextstrain/scratch/reference-only/examples.fasta
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>Demo sequence 1
ACGTGCGTACGTACGTACGTACGTACGTACGCGTACGTACGTACGTACGTACGTACGTACGTACGTACGTATGTACGTACGTACGTACGTACGTACGTACGTACGNNNGTACGTACGTACGTACGRACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
>Demo sequence 2
ACGTGCGTACGTACGTACGTACGTACGTACGCGTACGTACGTACGTACGTACGTACGTACGTACGTACGTATGTACGTACGTACGTACGTACGTACGTACGTACGNNNGTACGTACGTACGTACGRACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTANNNNACGTACGTACGTACGTACGTACGTACGTACGTACTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTATACGTACGTACGTACGTACGTACGTACGT
52 changes: 52 additions & 0 deletions data/nextstrain/scratch/reference-only/pathogen.json
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{
"alignmentParams": {
"excessBandwidth": 9,
"terminalBandwidth": 100,
"allowedMismatches": 4,
"gapAlignmentSide": "right",
"minSeedCover": 0.1
},
"compatibility": {
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
},
"files": {
"changelog": "CHANGELOG.md",
"pathogenJson": "pathogen.json",
"readme": "README.md",
"reference": "reference.fasta",
"examples": "examples.fasta"
},
"schemaVersion": "3.0.0",
"version": {
"tag": "unreleased"
},
"maintenance": {
"website": [
"https://nextstrain.org",
"https://clades.nextstrain.org"
],
"documentation": [
"https://github.com/nextstrain/nextclade_data",
"https://docs.nextstrain.org/projects/nextclade"
],
"source code": [
"https://github.com/nextstrain/nextclade_data",
"https://github.com/neherlab/nextclade_data_workflows"
],
"issues": [
"https://github.com/nextstrain/nextclade_data",
"https://github.com/nextstrain/nextclade_data/issues"
],
"organizations": [
"Nextstrain"
],
"authors": [
"Nextstrain team <https://nextstrain.org>"
]
},
"attributes": {
"name": "Scratch - Reference only",
"reference name": "None - Bring your own"
}
}
2 changes: 2 additions & 0 deletions data/nextstrain/scratch/reference-only/reference.fasta
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>Placeholder
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
55 changes: 55 additions & 0 deletions data_output/index.json
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Expand Up @@ -2015,6 +2015,61 @@
"web": "3.0.0-alpha.0"
}
}
},
{
"path": "nextstrain/scratch/reference-only",
"enabled": true,
"attributes": {
"name": "Scratch - Reference only",
"reference name": "None - Bring your own"
},
"maintenance": {
"website": [
"https://nextstrain.org",
"https://clades.nextstrain.org"
],
"documentation": [
"https://github.com/nextstrain/nextclade_data",
"https://docs.nextstrain.org/projects/nextclade"
],
"source code": [
"https://github.com/nextstrain/nextclade_data",
"https://github.com/neherlab/nextclade_data_workflows"
],
"issues": [
"https://github.com/nextstrain/nextclade_data",
"https://github.com/nextstrain/nextclade_data/issues"
],
"organizations": [
"Nextstrain"
],
"authors": [
"Nextstrain team <https://nextstrain.org>"
]
},
"files": {
"changelog": "CHANGELOG.md",
"pathogenJson": "pathogen.json",
"readme": "README.md",
"reference": "reference.fasta",
"examples": "examples.fasta"
},
"versions": [
{
"tag": "unreleased",
"compatibility": {
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
}
}
],
"version": {
"tag": "unreleased",
"compatibility": {
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
}
}
}
]
},
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