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Updated QC parameters
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jamessiqueirap committed Aug 13, 2024
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9 changes: 6 additions & 3 deletions data/community/v-gen-lab/dengue-lineages/denv1/README.md
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## Scope of this Dataset
This dataset is based on the dengue virus lineage system from [Verity 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 and contacts
## Authors

Maintainers: [James Siqueira Pereira](https://github.com/jamessiqueirap) and [Alex Ranieri](https://github.com/alex-ranieri).
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)

## Dengue Lineages System Project

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.

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.

## For Contact and bugs

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)

## What is Nextclade dataset

Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
8 changes: 5 additions & 3 deletions data/community/v-gen-lab/dengue-lineages/denv2/README.md
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## Scope of this Dataset
This dataset is based on the dengue virus lineage system from [Verity et al., 2024](https://doi.org/10.1101/2024.05.16.24307504) and is suitable for the analysis of DENV-2 viral sequences. The systems are independent, so sequences from other serotypes may not be classified or may be assigned as "Outgroup."

## Authors and contacts
## Authors

Maintainers: [James Siqueira Pereira](https://github.com/jamessiqueirap) and [Alex Ranieri](https://github.com/alex-ranieri).
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)

## Dengue Lineages System Project

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.

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.

## For Contact and bugs

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)

## What is Nextclade dataset

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7 changes: 5 additions & 2 deletions data/community/v-gen-lab/dengue-lineages/denv3/README.md
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## Authors and contacts

Maintainers: [James Siqueira Pereira](https://github.com/jamessiqueirap) and [Alex Ranieri](https://github.com/alex-ranieri).
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)

## Dengue Lineages System Project

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.

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.

## For Contact and bugs

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)

## What is Nextclade dataset

Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
9 changes: 6 additions & 3 deletions data/community/v-gen-lab/dengue-lineages/denv4/README.md
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## Scope of this Dataset
This dataset is based on the dengue virus lineage system from [Verity et al., 2024](https://doi.org/10.1101/2024.05.16.24307504) and is suitable for the analysis of DENV-4 viral sequences. The systems are independent, so sequences from other serotypes may not be classified or may be assigned as "Outgroup."

## Authors and contacts
## Authors

Maintainers: [James Siqueira Pereira](https://github.com/jamessiqueirap) and [Alex Ranieri](https://github.com/alex-ranieri).
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)

## Dengue Lineages System Project

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.

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.

## For Contact and bugs

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)

## What is Nextclade dataset

Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html

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