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‎data_output/index.json‎

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"treeJson": "tree.json"
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},
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"capabilities": {
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"clades": 5,
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"clades": 7,
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"customClades": {
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"outbreak": 1,
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"lineage": 33
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"missingData",
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"mixedSites",
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"privateMutations",
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"snpClusters",
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"stopCodons"
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]
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},
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"versions": [
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{
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"tag": "unreleased",
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"compatibility": {
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"cli": "3.0.0-alpha.0",
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"web": "3.0.0-alpha.0"
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}
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},
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{
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"updatedAt": "2024-04-19T07:50:39Z",
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"tag": "2024-04-19--07-50-39Z",
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}
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],
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"version": {
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"updatedAt": "2024-04-19T07:50:39Z",
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"tag": "2024-04-19--07-50-39Z",
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"tag": "unreleased",
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"compatibility": {
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"cli": "3.0.0-alpha.0",
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"web": "3.0.0-alpha.0"

‎data_output/nextstrain/mpox/all-clades/unreleased/CHANGELOG.md‎

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## Unreleased
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- Clade Ia and clade Ib are now distinguished
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- Sequences shared via Genbank since 2024 have been added

‎data_output/nextstrain/mpox/all-clades/unreleased/README.md‎

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# Nextclade dataset for "Mpox virus (All Clades)"
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| Key | Value |
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| ---------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| authors | [Cornelius Roemer](https://neherlab.org), [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org) |
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| data source | Genbank |
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| workflow | [github.com/nextstrain/mpox/nextclade](https://github.com/nextstrain/mpox/nextclade) |
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| nextclade dataset path | nextstrain/mpox/all-clades |
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| annotation | [NC_063383.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_063383) |
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| clade definitions | [github.com/mpxv-lineages/lineage-designation](https://github.com/mpxv-lineages/lineage-designation) |
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| related datasets | Mpox virus (Clade IIb): `nextstrain/mpox/clade-iib`<br>Mpox virus (Lineage B.1) `nextstrain/mpox/lineage-b.1`<br>Mpox virus (Clade I): `nextstrain/mpox/clade-i` |
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## Scope of this dataset
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This dataset is for Mpox viruses of all clades (Ia, Ib, IIa and IIb). For a focused analysis of sequences from clade IIb, you may want to use the more specific dataset: "Clade IIb" (`nextstrain/mpox/clade-iib`). For an even more focused analysis of 2022-2023 outbreak sequences (lineage B.1 and sublineages), you may want to use the even more specific dataset: "Lineage B.1" (`nextstrain/mpox/lineage-b.1`). For clade I sequences, you may want to use the dataset "Clade I" (`nextstrain/mpox/clade-i`).
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## Reference sequence and reference tree
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The reference used in this dataset is the clade IIb NCBI refseq `NC_063383.1` (Isolate `MPXV-M5312_HM12_Rivers`).
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Sequences for the reference tree come from NCBI/Genbank and are downsampled to around 900 sequences from the diversity of clades, lineages, countries and collection dates.
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## Further reading
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The lineage system used is described in [Happi et. al. (2022)](https://doi.org/10.1371/journal.pbio.3001769). Lineage definitions are available at [github.com/mpxv-lineages/lineage-designation](https://github.com/nextstrain/mpox/nextclade).
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Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

‎data_output/nextstrain/mpox/all-clades/unreleased/dataset.zip‎

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‎data_output/nextstrain/mpox/all-clades/unreleased/genome_annotation.gff3‎

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‎data_output/nextstrain/mpox/all-clades/unreleased/pathogen.json‎

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{
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"alignmentParams": {
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"excessBandwidth": 100,
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"terminalBandwidth": 300,
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"allowedMismatches": 8,
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"windowSize": 40,
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"minSeedCover": 0.1,
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"gapAlignmentSide": "left"
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},
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"attributes": {
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"name": "Mpox virus (All clades)",
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"reference accession": "NC_063383.1",
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"reference name": "MPXV-M5312_HM12_Rivers"
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},
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"compatibility": {
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"cli": "3.0.0-alpha.0",
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"web": "3.0.0-alpha.0"
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},
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"deprecated": false,
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"enabled": true,
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"experimental": false,
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"files": {
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"changelog": "CHANGELOG.md",
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"examples": "sequences.fasta",
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"genomeAnnotation": "genome_annotation.gff3",
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"pathogenJson": "pathogen.json",
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"readme": "README.md",
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"reference": "reference.fasta",
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"treeJson": "tree.json"
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},
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"official": true,
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"qc": {
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"frameShifts": {
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"enabled": true,
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"ignoredFrameShifts": [
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{
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"codonRange": {
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"begin": 3,
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"end": 589
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},
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"cdsName": "OPG003"
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},
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{
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},
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"cdsName": "OPG003_dup"
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},
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{
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},
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{
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},
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},
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{
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},
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"cdsName": "OPG180"
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},
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{
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"end": 101
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},
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"cdsName": "OPG197"
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},
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{
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},
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"cdsName": "OPG037"
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},
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{
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},
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"cdsName": "OPG037"
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},
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{
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},
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"cdsName": "OPG047"
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},
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},
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},
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},
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},
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{
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},
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},
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},
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"cdsName": "OPG153"
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},
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},
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},
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{
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},
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"cdsName": "OPG195"
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},
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{
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"codonRange": {
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},
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"cdsName": "OPG195"
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},
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{
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"codonRange": {
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"end": 346
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},
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"cdsName": "OPG174"
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}
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],
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"scoreWeight": 20
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},
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"missingData": {
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"enabled": true,
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"missingDataThreshold": 20000,
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"scoreBias": 1000
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},
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"mixedSites": {
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"enabled": true,
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"mixedSitesThreshold": 40
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},
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"privateMutations": {
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"cutoff": 300,
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"enabled": true,
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"typical": 50,
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"weightLabeledSubstitutions": 6,
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"weightReversionSubstitutions": 6,
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"weightUnlabeledSubstitutions": 1
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},
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"snpClusters": {
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"clusterCutOff": 5,
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"enabled": true,
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"scoreWeight": 10,
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"windowSize": 300
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},
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"stopCodons": {
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"enabled": true,
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"ignoredStopCodons": [
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{
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"codon": 187,
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"cdsName": "OPG015_dup"
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},
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{
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"codon": 187,
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"cdsName": "OPG015"
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},
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{
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"codon": 21,
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"cdsName": "OPG176"
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},
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{
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"codon": 299,
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"cdsName": "OPG187"
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},
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{
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"codon": 48,
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"cdsName": "OPG059"
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}
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],
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"scoreWeight": 20
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}
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},
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"schemaVersion": "3.0.0",
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"shortcuts": [
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"MPXV",
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"nextstrain/mpox"
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],
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"version": {
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"tag": "unreleased",
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"compatibility": {
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"cli": "3.0.0-alpha.0",
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"web": "3.0.0-alpha.0"
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}
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}
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}

‎data_output/nextstrain/mpox/all-clades/unreleased/reference.fasta‎

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‎data_output/nextstrain/mpox/all-clades/unreleased/sequences.fasta‎

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‎data_output/nextstrain/mpox/all-clades/unreleased/tree.json‎

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