NextStrain Community Analysis Repository

This repository is a central place to share and view Nextstrain phylogenetic analyses. It uses the nextstrain.org community sharing feature, which automatically serves datasets stored in this GitHub repository.

How It Works

The nextstrain.org platform is configured to monitor this repository. Any correctly formatted dataset files (.json) placed in the auspice/ directory on the main branch will automatically become available for viewing online.

The key is to follow a specific file naming convention, which determines the final URL for your dataset.

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How to Contribute a New Dataset

To add your own analysis results, please follow these steps.

1. Prepare Your Dataset File

After running your Nextstrain analysis, you will have an output JSON file located in the auspice/ directory of your build. This is the file you need to share (e.g., zika.json).

2. Rename Your File Correctly

This is the most important step. The filename must follow this format:

repository-name_part1_part2_..._partN.json

• repository-name: This must be the literal name of this repository, which is nextstrain-share.
• _part1_part2_...: These are underscore-separated names that describe your dataset. They will be converted into slash-separated parts in the final URL.

Example: If you have an analysis of Dengue Serotype 3, a good filename would be: nextstrain-share_dengue_serotype-3.json

3. Add the File to the Repository

Place your correctly named JSON file inside the auspice/ directory in this repository.

4. Submit Your Changes

If you have write access to this repo, you can commit the file directly. Otherwise, the best way to contribute is by opening a Pull Request:

1. Fork this repository.
2. Clone your fork to your local machine.
3. Create a new branch for your dataset (e.g., git checkout -b add-dengue-dataset).
4. Add your file to the auspice/ folder.
5. Commit and push your changes to your fork.
6. Open a Pull Request from your fork to this repository's main branch.

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Viewing Datasets

Once a dataset is merged into the main branch, it may take 5-10 minutes for it to become available on nextstrain.org due to caching.

The URL structure is: https://nextstrain.org/community/<USERNAME>/<REPO-NAME>@main/<PART1>/<PART2>

Example links

File in auspice/ directory	Resulting Nextstrain URL
nextstrain-share_mpox-analysis.json	nextstrain.org/community/LucvZon/nextstrain-share@main/mpox-analysis
nextstrain-share_zika.json	nextstrain.org/community/LucvZon/nextstrain-share@main/zika
nextstrain-share_dengue_serotype-3.json	.../nextstrain-share@main/dengue/serotype-3 (Hypothetical example)

To see a list of all available datasets, visit the base community URL: https://nextstrain.org/community/LucvZon/nextstrain-share@main

Sharing Narratives

The process is similar for sharing Nextstrain Narratives.

• Place your markdown file (.md) in the narratives/ directory.
• Follow the same file naming convention (nextstrain-share_my-narrative.md).
• The URL will be accessible under /narratives/.