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[D1.1] add to README
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jameshadfield committed Feb 23, 2025
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Expand Up @@ -63,6 +63,16 @@ This should allow any reassortments to be highlighted and will also include outb

> Note that generating any segment-level build here will necessarily build the genome tree, as it's needed to identify the clade of interest in each segment.
## H5N1 D1.1 Cattle outbreak (2025)

> This build is a work in progress and relies on recent improvements to ingest which add GenoFLU constellations to the metadata TSV
The H5N1-D1.1/genome build uses a similar approach to the H5N1 Cattle Outbreak above however samples all data to a GenoFLU constellation of D1.1.

```bash
snakemake --cores 1 -pf --configfile config/h5n1-d1.1.yaml
```


## Creating a custom build
The easiest way to generate your own, custom avian-flu build is to use the quickstart-build as a starting template. Simply clone the quickstart-build, run with the example data, and edit the Snakefile to customize. This build includes example data and a simplified, heavily annotated Snakefile that goes over the structure of Snakefiles and annotates rules and inputs/outputs that can be modified. This build, with it's own readme, is available [here](https://github.com/nextstrain/avian-flu/tree/master/quickstart-build).
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