nextclade
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nextstrain
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
I just got this bug and I have no idea what it means! Check spelling of what? This is the link I used: https://master.clades.nextstrain.org/?dataset-name=MPXV&input-fasta=https%3A%2F%2Fmpox-lapis.genspectrum.org%2Fv1%2Fsample%2Ffasta%3ForderBy%3Drandom%26limit%3D200%26country%3DUnited%2BKingdom%26yearFrom%3D2022%26downloadAsFile%3Dtrue I'm running this on Chrome on...
The currently deployed version links to non-existent v1 files. I decided to remove direct links, because we have many more platforms now, and only leave the link to GitHub Releases....
Resolves #932 Related https://github.com/cevo-public/cov-spectrum-website/issues/545 In this PR: - [x] calculate coverage QC metric as defined in the issues linked above - [x] add it to CSV and TSV output -...
`Coverage` is normally defined as number of valid called bases divided by length of the virus. Does Nextclade have a column for this? The only way I can seem to...
Matthijs Welkers made a good suggestion to make the primer feature more useful. Right now primer mutations are not surfaced in sequence view. We could surface them similar to how...
Matthijs Welkers mentioned that he had tried to use Nextclade's primer feature with monkeypox (he has published an amplicon tiling scheme for nanopore) but that he got an error when...
Right now we break up private mutations into: labeled, unlabeled and reversions. For monkeypox, I noticed that it would be nice to see sometimes if a mutation was simply already...
Brotli compresses datasets and wasm much better than gzip, it would be nice if we could take advantage of that. Using max compression comparison on SC2 tree and sample sequences,...
Background: My lab uses Illumina's COVIDSeq platform to sequence SARS-CoV-2 variants, including Illumina's BaseSpace sequencing analysis platform (DRAGEN COVID Lineage application), which utilizes NextClade for viral clade / mutation assessment....
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Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement