John Huddleston
John Huddleston
**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...
Fewer than 1% of strains sampled between 2017—2019 have ambiguous dates, but when these strains are included in a seasonal flu build, the pipeline assigns them two different effective dates....
We currently estimate tip frequencies up to the current date of a given build, but the latest available sequences are often collected one or two months prior to the current...
Source code for the binary "writeTrimmedRegionTable" is missing in the pbihdfutils subdirectory. This binary is built here: https://github.com/mchaisso/blasr/blob/master/pbihdfutils/Makefile#L75-L76
A common task in phylogenetics is to inspect the bootstrap support for individual nodes in a tree. Now that [Augur supports passing (some) bootstrap confidence values through to the Auspice...
### Description of proposed changes Adds the Jupyter notebook and corresponding restructured text version of a how-to guide to estimate clade frequencies from SARS-CoV-2 data. An open question with this...
While chatting with @jameshadfield about [a new `branch_labels` key for node data JSONs produced by `augur clades`](https://github.com/nextstrain/augur/pull/728), we realized that we don't currently document the node data JSON format anywhere....
As described in 4fb61d9 and [this comment on the install docs rewrite PR](https://github.com/nextstrain/docs.nextstrain.org/pull/52#issuecomment-834573018), we need to decide whether to use the `nextstrain` meta package from Bioconda to install all Nextstrain...
Adds a copy of the original Snakemake-based Zika tutorial from the Augur repository. This is part of an effort to refine the content of the Zika and TB tutorials to...
## Context As we develop more Nextclade datasets, we encounter a common pattern where we want to build a divergence tree for Nextclade instead of a time tree, but we...