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Hello, I'm trying to run a next strain analysis using gisaid data. (export augur needed data from gisaid). After exporting the data (fasta and metadata files). I made my own configuration file (attach…
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Part of my work involves comparing the results based on different definitions of variants. It would be nice to standardize this process.
- [x] [Constellations](https://github.com/cov-lineages/const…
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Hi there! I'm trying to set up Pyro-cov using GISAID but I don't have a data feed yet. It would be possible to use the pipeline with other data sources, like fasta files I have been downloaded? Would …
joicy updated
2 years ago
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Why I am getting below when I run the preprocessing script?
1323 sequences selected
searching fasta and writing sequences to output directory...
3679 sequences from input fasta processed
0 seq…
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I am trying to run the nextstrain pipeline, I did following steps but I am getting an error.
Step 1. I downloaded seasonal-flu repo and created a directory called "data/h3n2", and placed the fasta …
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Hi, @maximilianh
It's a useful tool for submitting viral sequences in bulk.
I am wondering to know if it was possible to provide submission of pathogenic sequences other than COVID-19 (e.g influe…
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Hi there,
Really excited to know this tool! Want to apply this pipeline to precess global contextual data from GISAID.
Question: How to prepare JSON dump from GISAID?
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Would save clicks (click, ctrl+a, copy) if the tip list had a "copy to clipboard" button :)
Using this very extensively now for pango designations :)
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### Context
Just trying out `augur curate`. First painpoint is that it doesn't seem to support `zst` compressed fasta (at least according to docs).
### Description
Support zst compressed input me…