This repository contains the public H5N1 cattle sequences deposited into the SRA by the USDA NVSL team. These raw reads were assembled and mapped by a team of people, and desposited in this github repo. I took these sequences, assigned clades with LABEL, and put them in Nextstrain format. Please feel free to use this however you wish.
This metadata is formatted such that it can be slotted into the avian-flu Nextstrain pipeline at the metadata.tsv stage. The cattle and bird sequences have been added to h5nx-clades.tsv and h5nx-clades.tsv, via manual annotation with LABEL. So LABEL clade annotations will be automatically and correctly added for these strains now.