John Huddleston
John Huddleston
## Context We produce monthly reports describing seasonal influenza circulation patterns. A substantial portion of time spent on these reports is tedious copying and pasting or running commands manually that...
### Current Behavior [Our current approach to joining segment-level metadata records into isolate-level metadata records](https://github.com/nextstrain/seasonal-flu/blob/d8bca3a5359c08d7a47522b3fe7fdee5f12c8b25/workflow/snakemake_rules/select_strains.smk#L49-L71) is an HA-centric one such that NA records without a matching HA do not get...
## Description of proposed changes Add measurements panel to H3N2 HA build for Welsh et al. escape scores grouped by serum or cohort. Enables interactive visualization and filtering of data....
## Context Despite our myriad quality filters in the workflow including a global clock rate filter, local clock rate filter, an outliers list, and dropping sequences with poor alignments, our...
## Context We currently assign clade labels to trees in our main phylogenetic workflow using the `augur clades` command and the influenza clade nomenclature TSVs. However, clade assignments vary for...
## 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...