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update pathogen.json
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@anna-parker
anna-parker committed Feb 6, 2025
1 parent 958925a commit cb22bc0
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14 changes: 7 additions & 7 deletions data/community/pathoplexus/cchfv/linked/L/README.md
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# Nextclade dataset for "Crimean-Congo hemorrhagic fever virus segment L" based on reference "NC_005301.3"

| Key | Value |
| ------------------- | ----------------------------------------------------------------------------------------------------------- |
| authors | Jessica Falkowski, [Richard Neher](https://neherlab.org), Anna Parker, [Nextstrain](https://nextstrain.org) |
| name | Crimean-Congo hemorrhagic fever virus segment L |
| reference | NC_005301.3 |
| dataset path | cchfv/linked/L |
| reference accession | |
| Key | Value |
| ------------------- | ------------------------------------------------------------------------------------------------------- |
| authors | Jessica Falkowski, [Richard Neher](https://neherlab.org), [Anna Parker](https://github.com/anna-parker) |
| name | Crimean-Congo hemorrhagic fever virus segment L |
| reference | NC_005301.3 |
| dataset path | cchfv/linked/L |
| reference accession | |

## Scope of this dataset

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24 changes: 22 additions & 2 deletions data/community/pathoplexus/cchfv/linked/L/pathogen.json
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Expand Up @@ -13,6 +13,11 @@
"changelog": "CHANGELOG.md"
},
"schemaVersion": "3.0.0",
"attributes": {
"name": "CCHF (segment L)",
"reference name": "Crimean-Congo hemorrhagic fever virus segment L",
"reference accession": "NC_005301.3"
},
"qc": {
"privateMutations": {
"enabled": true,
Expand All @@ -30,7 +35,7 @@
"snpClusters": {
"enabled": false,
"windowSize": 100,
"clusterCutOff": 12,
"clusterCutOff": 6,
"scoreWeight": 50
},
"mixedSites": {
Expand All @@ -39,7 +44,22 @@
},
"frameShifts": {
"enabled": true,
"ignoredFrameShifts": []
"ignoredFrameShifts": [
{
"cdsName": "RdRp",
"codonRange": {
"begin": 792,
"end": 795
}
},
{
"cdsName": "RdRp",
"codonRange": {
"begin": 3902,
"end": 3903
}
}
]
},
"stopCodons": {
"enabled": true,
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14 changes: 7 additions & 7 deletions data/community/pathoplexus/cchfv/linked/M/README.md
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# Nextclade dataset for "Crimean-Congo hemorrhagic fever virus segment M" based on reference "NC_005300.2"

| Key | Value |
| ------------------- | ----------------------------------------------------------------------------------------------------------- |
| authors | Jessica Falkowski, [Richard Neher](https://neherlab.org), Anna Parker, [Nextstrain](https://nextstrain.org) |
| name | Crimean-Congo hemorrhagic fever virus segment M |
| reference | NC_005300.2 |
| dataset path | cchfv/linked/M |
| reference accession | |
| Key | Value |
| ------------------- | ------------------------------------------------------------------------------------------------------- |
| authors | Jessica Falkowski, [Richard Neher](https://neherlab.org), [Anna Parker](https://github.com/anna-parker) |
| name | Crimean-Congo hemorrhagic fever virus segment M |
| reference | NC_005300.2 |
| dataset path | cchfv/linked/M |
| reference accession | |

## Scope of this dataset

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6 changes: 6 additions & 0 deletions data/community/pathoplexus/cchfv/linked/M/pathogen.json
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"alignmentParams": {
"minSeedCover": 0.01,
"kmerLength": 7,
"allowedMismatches": 10,
"retryReverseComplement": true
},
"files": {
Expand All @@ -14,6 +15,11 @@
"changelog": "CHANGELOG.md"
},
"schemaVersion": "3.0.0",
"attributes": {
"name": "CCHF (segment M)",
"reference name": "Crimean-Congo hemorrhagic fever virus segment M",
"reference accession": "NC_005300.2"
},
"qc": {
"privateMutations": {
"enabled": true,
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14 changes: 7 additions & 7 deletions data/community/pathoplexus/cchfv/linked/S/README.md
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# Nextclade dataset for "Crimean-Congo hemorrhagic fever virus segment S" based on reference "NC_005302.1"

| Key | Value |
| ------------------- | ----------------------------------------------------------------------------------------------------------- |
| authors | Jessica Falkowski, [Richard Neher](https://neherlab.org), Anna Parker, [Nextstrain](https://nextstrain.org) |
| name | Crimean-Congo hemorrhagic fever virus segment S |
| reference | NC_005302.1 |
| dataset path | cchfv/linked/S |
| reference accession | |
| Key | Value |
| ------------------- | ------------------------------------------------------------------------------------------------------- |
| authors | Jessica Falkowski, [Richard Neher](https://neherlab.org), [Anna Parker](https://github.com/anna-parker) |
| name | Crimean-Congo hemorrhagic fever virus segment S |
| reference | NC_005302.1 |
| dataset path | cchfv/linked/S |
| reference accession | |

## Scope of this dataset

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7 changes: 6 additions & 1 deletion data/community/pathoplexus/cchfv/linked/S/pathogen.json
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Expand Up @@ -14,6 +14,11 @@
"changelog": "CHANGELOG.md"
},
"schemaVersion": "3.0.0",
"attributes": {
"name": "CCHF (segment S)",
"reference name": "Crimean-Congo hemorrhagic fever virus segment S",
"reference accession": "NC_005302.1"
},
"qc": {
"privateMutations": {
"enabled": true,
Expand All @@ -31,7 +36,7 @@
"snpClusters": {
"enabled": false,
"windowSize": 100,
"clusterCutOff": 12,
"clusterCutOff": 6,
"scoreWeight": 50
},
"mixedSites": {
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