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## Context
Prior to the SARS-CoV-2 pandemic, we assumed that Nextstrain workflows would begin with pre-curated sequences and metadata sourced either from our internal database ("fauna") or custom s…
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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…
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**Context**
I've been running builds locally to get context surrounding 21K viruses and I'd like to again flag `augur filter` subsampling as a major performance bottleneck. Here, I'm starting fro…
trvrb updated
1 month ago
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Now that I've done the RAM upgrade, we should restore the data processing workflow on the cluster
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For new lineages, the 3d delay between GISAID and covSpectrum is often critical so I go and check on GISAID directly.
Unfortunately, GISAID uses different AA names, so it's quite tedious to create …
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There may be an emerging JN.1 sublineage with ORF1a:T170I (NSP1:T170I; C774T), ORF1b:G662S (NSP12:G671S; G15451A), T18453C first detected in Denmark.
If this sublineage is designated, I recommend t…
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I'm trying to figure out how to use Nextclade CLI. I follow all the directions, but nothing ever seems to work. For example, after trying to run a fasta multiple times, the error messages indicated I …
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At some point (possibly associated with the migration, not sure) this problem came up recently. There are about 150 sequences in the fasta but doesn't have associated metadata in the database. The lis…