seasonal-flu
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nextstrain
Scripts. config, and snakefiles for seasonal-flu nextstrain builds
Follow up to https://github.com/nextstrain/seasonal-flu/pull/126 Will need to look through [netlify-cli's changelog](https://github.com/netlify/cli/blob/main/CHANGELOG.md) to figure out what has changed between 17.2.2 and 17.5.1 (or later).
### Context I am working on using Nextstrain for global surveillance of Influenza. As part of our bioinformatics workflow, we already assign each sequenced virus to a clade (e.g., 3C.2a1b.2a.2)...
@corneliusroemer experimented with [IQ-TREE's constraint tree option](http://www.iqtree.org/doc/Advanced-Tutorial#constrained-tree-search) to prevent IQ-TREE from putting clades in the wrong place for NextClade reference trees. This seems like a good way to ensure correct...
I think there's a minor typo in the README: > These antigenic data come in four flavors depending on the assay that passage history of the antigens. Should possibly be:...
## Context In the near future, we would like to support region-specific flu builds and also enable other researchers to use this repository to define their own custom flu builds...
**Context** Phylogenetic trees of HA/NA help us identify emerging clades that should be tracked by routine surveillance. For each of these emerging clades, we need a way to identify candidate...
**Context** We currently define clades for all Nextstrain flu builds using the same manually curated clade definition files. However, for surveillance purposes, it would be helpful to have a way...
**Current Behavior** The time tree view on nextflu works as expected:  When one deselects the "timetree" option to view the divergence tree, the tree collapses to one position on...
**Context** To enable SARS-CoV-2 narratives based on data at specific timepoints, [we've maintained dated Auspice JSONs that are automatically generated as part of the standard Nextstrain workflow](https://github.com/nextstrain/ncov/blob/5509eaf0805708306c61f48228a75bd3d0649ddf/workflow/snakemake_rules/export_for_nextstrain.smk#L126-L141). These dated builds...
**Current Behavior** Titer records define strain names for test and reference viruses, but we do not automatically cross-check these names with existing names in GISAID/GenBank records. As a result, there...
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Scripts. config, and snakefiles for seasonal-flu nextstrain builds