pangolin

Phylogenetic Assignment of Named Global Outbreak LINeages

Requirements

Pangolin runs on MacOS and Linux. The conda environment recipe may not build on Windows (I haven't tested it) but can be run using the Windows subsystem for Linux.

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

Install pangolin

1. Clone this repository and cd pangolin
2. conda env create -f environment.yml
3. python setup.py install or pip install .
4. That's it

Usage

1. Activate the environment conda activate pangolin
2. Run pangolin <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	UFbootstrap
Virus1	B.1	82
Virus2	A.1	95
Virus3	A.3	100
Virus4	B.1.4	73

Authors

Pangolin was created by Áine O'Toole and JT McCrone. It uses lineages from Rambaut, Holmes & Pybus.

References

The following external software is run as part of pangolin:

iqtree

L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies.. Mol. Biol. Evol., 32:268-274. https://doi.org/10.1093/molbev/msu300

D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, L.S. Vinh (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35:518–522. https://doi.org/10.1093/molbev/msx281

mafft

Katoh, Standley 2013 (Molecular Biology and Evolution 30:772-780) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. (outlines version 7)

snakemake

Köster, Johannes and Rahmann, Sven. “Snakemake - A scalable bioinformatics workflow engine”. Bioinformatics 2012.