From dd107cd593ee9b475a1e134e981b634119cebf35 Mon Sep 17 00:00:00 2001 From: james hadfield Date: Mon, 24 Feb 2025 09:45:48 +1300 Subject: [PATCH] [D1.1] add to README --- README.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/README.md b/README.md index 86049f0..1fedba5 100755 --- a/README.md +++ b/README.md @@ -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).