nextclade
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Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
It seems that Nextclade web may not necessarily get faster after a certain number of threads is reached. In particular, it may even get slower, as the setup time seems...
Many parts of the docs are SARS-CoV-2 specific. It would be good, if all SC2 specifics were put in boxes to not confuse readers who may only be interested in...
Right now, we only categorize private substitutions into a) reversions, b) labeled, c) unlabeled. Since true reversions of deletions are very unlikely (unless there's contamination/coinfection/recombination) they contain valuable QC/recombinant-detection information....
(Monkey testing find: Funny bug that's actually somewhat of a realisation of feature request #639 and thus useful) When going back and forth under certain circumstances (unlikely to be encountered...
I've often wished there was a way for the nextclade web interface to import a pre-computed nextclade analysis that comes from nextclade CLI output and/or saved as a serialized file...
Raised by Ricky Sucgang on Spheres Zoom In the mutation summary tooltip, we currently show nuc and aa mutations as separate lists. It would be nice to match them up....
Currently, nextclade CLI provides a nice tabular output file describing, for each genome, the observed non-synonymous SNPs and indels. Currently: - it does not describe synonymous SNPs - it has...
When there are mutations in the first or last 0.1% of the genome (e.g. pos 10 in SC2), they are not as visible as they should be because they crash...
I have a sequence that's reported to have 11 mutations in a cluster, but I can't figure out where this cluster is supposed to be. It would be helpful in...
Right now, we calculate mutation counts as raw nucleotide substitutions output by Nextalign. When there are regions of Ns, we therefore systematically underestimate the real divergence of sequences. A better...
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Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement