nextclade
nextclade copied to clipboard
nextstrain
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
It could be more useful to list reversion and labeled mutation counts rather than total nuc substitutions as a column. This would be a good place to add descriptive text...
Ambiguous nucleotides are currently displayed only in the tooltip of the corresponding column:  In gene view, ambiguous bases turn the corresponding AA into an X. It would be nice,...
Investigating EPI_ISL_8927255, I noticed that when there are ambiguous nucleotides in the query sequence at sites that are mutated in the nearest reference tree node, we falsely call this as...
Hi there, Thanks for considering the detection of frame shifts in the new release! I was wondering whether there is a way of translating the whole gene when there is...
Here's a user who was confused by the fact that running Nextclade with example sequences outputs a warning: ``` [WARN] Nextclade: Warning: in sequence "USA/VA-DCLS-3814/2021": When processing gene "ORF6": Unable...
When investigating whether a particular sequences is a contaminant or recombinant, I need to take that sequence in question and spike in some other clades like Delta, Alpha etc. This...
I uploaded a SARS-CoV-2 sequence to nextclade. Nextclade result shows two deletions, but I do not understand the visualized output in nextclade. The nextclade output is shown below. ...
I noticed that every time [augur](https://github.com/nextstrain/augur/blob/master/.github/workflows/ci.yaml) and [auspice](https://github.com/nextstrain/auspice/blob/master/scripts/rebuild-docker-image.sh) get updated, it triggers [a rebuild of the `nextstrain/base` Docker image](https://app.travis-ci.com/github/nextstrain/docker-base/builds). Would it be reasonable to add a trigger to this repository...
Nextclade lets users know how many private mutations are in a sequence but it would be great if it could generate a list of these private mutations. This could be...
When scrolling more than a few lines per second, the display is grey for a good part of a second. This seems to be due to lazy loading of the...
Metadata
Owner
Metadata
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement