chore: rebuild

data_output/community/moncla-lab/iav-h5/ha/2.3.4.4/unreleased/CHANGELOG.md

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+## Unreleased
+
+Updated private mutation QC metrics such that the typical value is the median value and the cutoff is the 97.5th percentile of private mutation counts assigned to unique GISAID sequences.
+
+## 2024-11-19T14:18:53Z
+
+Updated tree.json to add mutation calling relative to A/American_wigeon/North_Carolina/AH0182517/2022
+
+## 2024-05-08T11:39:52Z
+
+Initial release for Nextclade v3!
+
+Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

data_output/community/moncla-lab/iav-h5/ha/2.3.4.4/unreleased/README.md

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+# H5Nx clade `2.3.4.4` dataset with A/Astrakhan/3212/2020 reference
+
+| attribute            | value                                    |
+| -------------------- | ---------------------------------------- |
+| authors              |[Jordan Ort](https://lmoncla.github.io/monclalab/team/JordanOrt/), [Louise Moncla](https://lmoncla.github.io/monclalab/team/LouiseMoncla/)|
+| dataset name         | H5Nx clade `2.3.4.4` (provisional)         |
+| reference strain     | A/Astrakhan/3212/2020(H5N8)              |
+| reference accession  | EPI1846961                               |
+
+
+## Authors and contacts
+
+Maintained by: [Jordan Ort](https://lmoncla.github.io/monclalab/team/JordanOrt/)
+
+With the help from: [Louise Moncla](https://lmoncla.github.io/monclalab/team/LouiseMoncla/), Todd Davis, Tommy Lam, Samuel Shephard, Richard Neher
+
+## Scope of this dataset
+This dataset uses a current H5 candidate vaccine virus (CVV) from clade `2.3.4.4` (A/Astrakhan/3212/2020) as a reference and is suitable for the analysis of H5 sequences belonging to clade `2.3.4.4` and its sub-clades `2.3.4.4a` through `2.3.4.4h`. Sequences belonging to other clades cannot be annotated by this dataset and will be left `unassigned`.
+
+## Features
+This dataset supports
+
+ * Assignment to clades and subclades based on the provisional nomenclature defined by the WHO/FAO/WOAH H5 Nomenclature Working Group
+ * Sequence quality control (QC)
+ * Phylogenetic placement
+ * Annotations for glycosylation sties, HA cleavage site sequence, and presence/absence of a polybasic cleavage site
+
+
+## Clades of H5Nx avian influenza viruses
+
+The WHO/FAO/WOAH H5 Nomenclature Working Group define "clades" using HA gene seguences, and define clades as genetically distinct, monophyletic groups of viruses. Viruses falling into a given clade share a common ancestor with significant bootstrap support and have low levels of within-clade diversity. [Past nomenclature updates](https://onlinelibrary.wiley.com/doi/10.1111/irv.12324) have required viruses in the same clade to be monophyletic with bootstrap suppor of at least 60%, with within-clade pairwise distances of less than 1.5%. These requirements are sometimes relaxed, and clades are periodically updated to account for expanding viral diversity.
+
+Since 2006, clade `2.3.4.4` viruses have circulated continuously and diversified extensively into multiple sub-clades. To account for this expansion, clade `2.3.4.4` is being split into eight additional sub-clades, named `2.3.4.4a` through `2.3.4.4h` due to high circulating diversity within the clade.
+
+This Nextclade dataset incorporates these provisional `2.3.4.4` sub-clades.
+
+## Alternative, and complementary approaches for H5 clade assignment
+Two additional tools exist for assigning clades to H5 viruses that accommodate the recent `2.3.4.4` clade splits.
+
+1. [LABEL](https://wonder.cdc.gov/amd/flu/label/): this command-line tool is built and maintained by Sam Shepard, and performs clade assignment for all current `2.3.4.4` and `2.3.2.1` clade splits.
+2. [BVBRC Subspecies Classification Tool](https://www.bv-brc.org/app/SubspeciesClassification): this is a drag and drop tool that classifies a variety of viruses, including influenza A H1N1, H3N2, and H5N1.
+
+The clade assignments in this Nextclade dataset were validated against LABEL assignments and shown to be generally well-matched across subclades. The figure below shows a direct comparison of assignments for 1883 HA sequences from GISAID, performed using LABEL and this NextClade dataset for clade `2.3.4.4` and its subclades.
+
+![Figure 1: Comparison between LABEL and Nextclade for 2.3.2.1 assignments](https://raw.githubusercontent.com/moncla-lab/h5nx-Clades/main/jordan-h5-clades/testing-nextclade-datasets/2344/files/20240430_2344.png)
+
+## What is Nextclade dataset
+
+Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html