chore: rebuild [skip ci]

Author: nextstrain-bot

data_output/community/v-gen-lab/dengue/denv1/unreleased/README.md

@@ -1,32 +1,35 @@
-# Nextclade dataset for "DENV-1 Lineages" based on reference "Nauru/NMRI-45AZ5PDK-0/1974"
+# Nextclade Dataset for "DENV-1" Based on Reference "Nauru/NMRI-45AZ5PDK-0/1974"
 
+## Dataset Attributes
 
-## Dataset attributes
-
-| attribute            | value                                    |
+| Attribute            | Value                                    |
 | -------------------- | ---------------------------------------- |
-| name                 | DENV-1                                   |
-| refName              | Nauru/NMRI-45AZ5PDK-0/1974               |
-| refAccession         | NC_001477.1                              |
+| Name                 | DENV-1                                   |
+| RefName              | Nauru/NMRI-45AZ5PDK-0/1974               |
+| RefAccession         | NC_001477.1                              |
+
+## Scope of This Dataset
 
-## Scope of this Dataset
 This dataset is based on the dengue virus lineage system from [Hill et al., 2024](https://doi.org/10.1101/2024.05.16.24307504) and is suitable for the analysis of DENV-1 viral sequences. The systems are independent, so sequences from other serotypes may not be classified or may be assigned as "Outgroup."
 
-## Authors
+## Dengue Lineages System Project
+
+This system is built on experience developing lineage systems for other viruses of public health importance and is the result of a global collaboration of researchers and public health professionals. It aims to provide additional spatial and temporal resolution to discuss the large genetic diversity of the dengue virus. Specifically, it splits existing genotypes into smaller groups and provides a standardized, neutral naming system.
 
-Maintainers: [James Siqueira Pereira](https://github.com/jamessiqueirap) and [Alex Ranieri](https://github.com/alex-ranieri).
+Broadly speaking, we define major and minor lineages within each genotype. These lineages are defined by the same rules but use different nomenclature. In theory, minor lineages should be more useful for country-specific questions, and major lineages for regional questions. Of course, it won't necessarily always work like that—some minor lineages are very widespread, and some major lineages are geographically limited.
 
-## Dengue Lineages System Project
+The source code is available at [V-GEN-Lab/dengue-lineages-workflow](https://github.com/V-GEN-Lab/dengue-lineages-workflow).
+
+For bugs, please open an [issue](https://github.com/V-GEN-Lab/dengue-lineages-workflow/issues).
 
-This system is built off experience developing lineage systems for other viruses of public health importance, and is the result of a global collaboration of researchers and public health professionals. It aims to provide additional spatial and temporal resolution with which to discuss the large genetic diversity of dengue virus. Specifically, it splits up existing genotypes into smaller groups and provides a standardized, neutral naming system.
+## Maintainers and Contacts:
 
-Broadly speaking, we define major and minor lineages within each genotype. These lineages are defined by the same rules, but use different nomenclature. In theory, minor lineages should be more useful for country-specific questions, and major lineages for regional questions. Of course, it won't always necessarily work like that - some minor lineages are very widespread, and some major lineages are geographically limited.
+[James Siqueira Pereira](https://github.com/jamessiqueirap)¹ ² and [Alex Ranieri](https://github.com/alex-ranieri)¹.
 
-## For Contact and bugs
+## Affiliations
 
-The source code is avalible on [V-GEN-Lab/dengue-lineages-nextclade](https://github.com/V-GEN-Lab/dengue-lineages-nextclade)
-For bugs, please open an [Issue](https://github.com/V-GEN-Lab/dengue-lineages-nextclade/issues)
+¹ Center for Viral Surveillance and Serological Assessment [(CeVIVAS)](https://bv.fapesp.br/en/auxilios/110575/continuous-improvement-of-vaccines-center-for-viral-surveillance-and-serological-assessment-cevivas/) at the [Butantan Institute](https://en.butantan.gov.br/).
 
-## What is Nextclade dataset
+² University of São Paulo [(USP)](https://www5.usp.br/english/institutional/).
 
-Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
+Read more about Nextclade datasets in the Nextclade documentation: [Nextclade Datasets](https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html).

data_output/community/v-gen-lab/dengue/denv1/unreleased/dataset.zip

@@ -2,8 +2,7 @@
 ##source-version geneious 2022.2.2
 ##sequence-region	NC_001477.1	1	10735
 NC_001477.1	Geneious	gene	95	436	.	+	.	gene_name=C
-NC_001477.1	Geneious	gene	437	934	.	+	.	gene_name=M
-NC_001477.1	Geneious	gene	437	709	.	+	.	gene_name=pr
+NC_001477.1	Geneious	gene	437	934	.	+	.	gene_name=prM
 NC_001477.1	Geneious	gene	935	2419	.	+	.	gene_name=E
 NC_001477.1	Geneious	gene	2420	3475	.	+	.	gene_name=NS1
 NC_001477.1	Geneious	gene	3476	4129	.	+	.	gene_name=NS2A

data_output/community/v-gen-lab/dengue/denv1/unreleased/genome_annotation.gff3

@@ -1,6 +1,6 @@
 {
   "attributes": {
-    "name": "DENV-1 lineages",
+    "name": "DENV-1",
     "reference accession": "NC_001477.1",
     "reference name": "Nauru/NMRI-45AZ5PDK-0/1974"
   },