From 56b3ce8d7f0f83966f637f472f370fd6fb8b6504 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Fri, 9 Aug 2024 10:42:45 -0700 Subject: [PATCH 1/2] description: Update GitHub URLs - future proof by switching `master` to `-` - update URL for the clades.tsv to reflect move to `phylogenetic/` --- phylogenetic/defaults/description.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/phylogenetic/defaults/description.md b/phylogenetic/defaults/description.md index 816ba3b..b7016c3 100644 --- a/phylogenetic/defaults/description.md +++ b/phylogenetic/defaults/description.md @@ -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) From cd6bec0dd0782a25aa0b3c02a2512133271004ec Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Fri, 9 Aug 2024 10:50:50 -0700 Subject: [PATCH 2/2] description: Add link to clade I build --- phylogenetic/defaults/description.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/phylogenetic/defaults/description.md b/phylogenetic/defaults/description.md index b7016c3..558e663 100644 --- a/phylogenetic/defaults/description.md +++ b/phylogenetic/defaults/description.md @@ -1,6 +1,6 @@ We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain. -We maintain three views of MPXV evolution: +We maintain four views of MPXV evolution: The first is [`mpox/lineage-B.1`](https://nextstrain.org/mpox/lineage-B.1), which focuses on lineage B.1 of the global outbreak that started in 2022 and includes as many sequences as possible. Here, we conduct a molecular clock analysis in which evolutionary rate is estimated from the data (with a resulting estimate of ~6 × 10-5 subs per site per year). @@ -8,6 +8,8 @@ The second is [`mpox/clade-IIb`](https://nextstrain.org/mpox/clade-IIb), which f The third is [`mpox/all-clades`](https://nextstrain.org/mpox/all-clades), which focuses on broader viral diversity and includes viruses from the animal reservoir and previous human outbreaks, encompassing clades I, IIa and IIb as described in [Happi et al](https://doi.org/10.1371/journal.pbio.3001769) and endorsed by a [WHO convened consultation](https://worldhealthorganization.cmail20.com/t/ViewEmail/d/422BD62D623B6A3D2540EF23F30FEDED/F75AF81C90108C72B4B1B1F623478121?alternativeLink=False). +The fourth is [`mpox/clade-I`](https://nextstrain.org/mpox/clade-I), which focuses on clade I sequences and includes as many sequences as possible. + #### Analysis Our bioinformatic processing workflow can be found at [github.com/nextstrain/mpox](https://github.com/nextstrain/mpox) and includes: - sequence alignment by [nextalign](https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextalign-cli.html)