Phylogenetic Assignment of Named Global Outbreak LINeages
- Some version of conda, we use Miniconda3. Can be downloaded from here
- Your query fasta file
- Clone this repository
conda env create -f environment.yml
- That's it
- Activate the environment
conda activate pangolin-env
- Run
lineage <query>
pangolin: Phylogenetic Assignment of Named Global Outbreak LINeages
usage: pangolin <query> [options]
optional arguments:
-h, --help show this help message and exit
-o OUTDIR, --outdir OUTDIR
-n, --dry-run
-f, --force
-t THREADS, --threads THREADS
-u, --unlock
Your output will be a csv file with taxon name and lineage assigned, one line corresponding to each sequence in the fasta file provided
Example:
Taxon | Lineage |
---|---|
Virus1 | B.1 |
Virus2 | A.1 |
Virus3 | A.3 |
Virus4 | B.1.4 |