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Resources for a lineage naming scheme for SARS-CoV-2/hCoV-2019

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pangolin

Phylogenetic Assignment of Named Global Outbreak LINeages

Requirements

  1. Some version of conda, we use Miniconda3. Can be downloaded from here
  2. Your query fasta file

Install pangolin

  1. Clone this repository
  2. conda env create -f environment.yml
  3. That's it

Usage

  1. Activate the environment conda activate pangolin-env
  2. 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

Output

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

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