John Huddleston

seasonal flu "virus" records should be indexed by isolate id instead of strain name

1

## Description We currently [index the `virus` table in RethinkDB on the strain name of each isolate](https://github.com/nextstrain/fauna/blob/23e57d640905fdd5b5b86f2d6b8b1ff77e7cc27b/vdb/upload.py#L80). However, this indexing causes at least two problems: 1. sequence records can get...

## Description of proposed changes ### Overview This PR adds logic to annotate user-defined haplotypes in the phylogenetic workflow using Nextclade annotations and adds corresponding configuration files to define "emerging...

## Context Nextclade references that appear on clades.nextstrain.org live in this repository in the `nextclade/dataset_config/` directory. In principle, users can point their build configurations at these files, to run the...

## Context We allow users to define their own `reference` FASTA and `annotation` GFF in their build configurations. However, clade and subclade definitions use nucleotide positions from a specific reference...

## Context From @trvrb [on Slack](https://bedfordlab.slack.com/archives/C0K3GS3J8/p1734571859255039?thread_ts=1734549449.049429&cid=C0K3GS3J8): > seasonal flu, we have epitope mutations for [H3N2](https://nextstrain.org/seasonal-flu/h3n2/ha/2y?c=ep) and [H1N1pdm](https://nextstrain.org/seasonal-flu/h1n1pdm/ha/2y?c=ep), but strangely we don't have just HA1 mutations. (I no longer believe our...

## Description The current quickstart guide for using GISAID data assumes that users will download a single metadata XLS file and a single sequences FASTA file. However, GISAID limits the...

## Context Only H3N2 and H1N1pdm currently have Nextclade datasets for all 8 gene segments, while B/Vic has HA and NA datasets and B/Yam only has HA. The default HA...

Rename H3 proposed subclades

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Rename H3 subclade proposals for J.2 to use amino acid substitutions instead of single-letter suffixes. Test URL: https://clades.nextstrain.org?dataset-name=flu_h3n2_ha&dataset-url=https://github.com/nextstrain/nextclade_data/tree/rename-h3-proposed-subclades/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased

Add a map of Nextstrain clade to Pango lineage

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## Description of proposed changes Adds an official map between Nextstrain clade and Nextclade pango lineage to support analyses that need to convert between these two lineage naming systems. [Inspired...

Ingest from INSDC

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## Context [Avian influenza analyses ingest INSDC data](https://github.com/nextstrain/avian-flu/tree/master/ingest/build-configs/ncbi). Additionally, [the Oropouche ingest](https://github.com/nextstrain/oropouche/tree/main/ingest) includes [logic to group multiple segments of the same isolate](https://github.com/nextstrain/oropouche/blob/main/ingest/scripts/group_segments.py). [GenSpectrum maintains curated INSDC data for seasonal influenza](https://loculus.genspectrum.org/h3n2/search?orderBy=ncbiReleaseDate&page=1&order=descending)...