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description: Update GitHub URLs
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- future proof by switching `master` to `-`
- update URL for the clades.tsv to reflect move to `phylogenetic/`
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joverlee521 committed Aug 9, 2024
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4 changes: 2 additions & 2 deletions phylogenetic/defaults/description.md
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Expand Up @@ -14,11 +14,11 @@ Our bioinformatic processing workflow can be found at [github.com/nextstrain/mpo
- masking several regions of the genome, including the first 1350 and last 6422 base pairs and multiple repetitive regions of variable length
- phylogenetic reconstruction using [IQTREE-2](http://www.iqtree.org/)
- ancestral state reconstruction and temporal inference using [TreeTime](https://github.com/neherlab/treetime)
- clade assignment via [clade definitions defined here](https://github.com/nextstrain/mpox/blob/master/defaults/clades.tsv), to label broader MPXV clades I, IIa and IIb and to label hMPXV1 lineages A, A.1, A.1.1, etc...
- clade assignment via [clade definitions defined here](https://github.com/nextstrain/mpox/blob/-/phylogenetic/defaults/clades.tsv), to label broader MPXV clades I, IIa and IIb and to label hMPXV1 lineages A, A.1, A.1.1, etc...

#### Underlying data
We curate sequence data and metadata from the [NCBI Datasets command line tools](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/),
using an NCBI Taxonomy ID defined in [ingest/defaults/config.yaml](https://github.com/nextstrain/mpox/blob/master/ingest/defaults/config.yaml), as starting point for these analyses.
using an NCBI Taxonomy ID defined in [ingest/defaults/config.yaml](https://github.com/nextstrain/mpox/blob/-/ingest/defaults/config.yaml), as starting point for these analyses.

Curated sequences and metadata are available as flat files at:
- [data.nextstrain.org/files/workflows/mpox/sequences.fasta.xz](https://data.nextstrain.org/files/workflows/mpox/sequences.fasta.xz)
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