Hi @eam,
I ran into the exact issue with ingesting avian-flu H5N1sequences not having segment
in the metadata. I ended up using a combination of NCBI Datasets and NCBI Virus. You can find the workflow for at avian-flu/ingest/build-configs/ncbi/rules/fetch_from_ncbi.smk at master · nextstrain/avian-flu · GitHub.
Best,
Jover