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Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
Back in the day, when datasets description objects were very small, I decided (lazily) to store in the local storage the dataset object as-is, as it comes from the index.json....
Reported by @tsibley [here](https://github.com/nextstrain/nextclade/pull/1455#issuecomment-2140691617) > For me, the "Suggest automatically" feature of Nextclade was enabled by default (though it seems like a sticky preference?). With it enabled: > > 1....
Reported by @tsibley [here](https://github.com/nextstrain/nextclade/pull/1455#issuecomment-2140691617) > External datasets like this are tagged "community", e.g. > >  > > and while _I_ get why this is, it feels potentially pretty confusing...
On Nextstrain site that use auspice we make it clear that users can use screenshots/images of things from the website with an open license. It might be useful to users...
We want to add clickable links into mutation tooltips. These links would lead to the corresponding mutation view in nextstrain.org/ncov colored by the mutated nucleotide. For example, the mutations at...
Currently exported results only contain an array of results themselves. For better reproducibility and tracking it would be nice to save not only results themselves, but also input parameters used...
Make column names in CSV export more consistent: rename totalGaps to totalDeletions mutations - totalMutations insertions - totalInsertions missing - totalMissing
Hi, Do you provide any resource for the list of mutational changes per clade? In the dataset that is acquired with Nextclade CLI, `nextstrain/sars-cov-2/wuhan-hu-1`, there is this statement in README.md:...
Resolves: #1513 - [x] add a new column/field "cdsCoverage" to the output files - [x] add CDS coverage table in the tooltip of the "Cov." column in Nextclade Web
Motivated by https://github.com/nextstrain/pathogen-repo-guide/issues/50: > It seems like a common pattern for sequencing efforts to focus on specific genes instead of the full genome. It would be helpful for ingest to...
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Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement