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Dear @priesgo
While going through the pipeline, I realized that the VCF2FASTA does not masks the regions of low coverage. In amplicon sequencing data, there might be regions deprived of reads. I t…
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Currently the python scripts in the `./scripts/` folder do not seem to strictly follow any linting, formatting, typing or style guide, docstrings are often missing and no configuration files to ensure…
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I propose the following schema for the input CSV files:
https://github.com/averagehat/pux-starter-app/blob/sequence-db/schema.md
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@joverlee521 ---
There are a small handful of upstream fixes we need to shipping views.
1. The `date` field in `v2/shipping/augur-build-metadata` was formatted as `2019-09-25T19:37:35.483+00:00`…
trvrb updated
4 years ago
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The list of supported clades, which is written down in `mappings.csv`, was taken from nextclade-data, and contains three Delta clades: 21A, 21I and 21J. The latter two do not map to single pango linea…
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### Context
Previously mentioned in https://github.com/nextstrain/augur/pull/1039#issuecomment-1252912107 and https://github.com/nextstrain/augur/issues/1475.
A lot of public health folks use …
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One to file under 'project proposal'/suggestion...
Is there enough sequencing data, spread around the world to enable variants to be identified that appear to be 'winning' the evolution race compa…
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**Context**
As I'm writing the weekly situation reports, it would be a *huge* help to be able to deep link to a view of the tree that's zoomed into any arbitrary node, rather than having to define …
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**Describe the bug**
This may be a bug in the JSON produced by the UShER web interface, not Galago, but they're not working together yet so let's figure it out.
**Expected behavior / How to repr…
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**Context**
TREETime is a computational bottleneck in the Augur bioinformatic pipeline, especially when modeling thousands and thousands of raw genomic data.
Bottom line up, how to have Augur ab…