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For users who want to use GISAID data with this workflow, the following steps work _nearly_ as expected.
These steps assume you have downloaded:
- all sequences in FASTA format with whitespace …
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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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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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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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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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## New lineage proposal
by
### Description
Sub-lineage of:
Earliest sequence:
Most recent sequence:
Countries circulating:
### Genomes
### Evidence
### Proposed lineage …
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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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