An open-source pipeline to construct a global phylogeny of the plague pathogen Yersinia pestis.

Pipeline Overview

1. Create a metadata database of NCBI genomic assemblies and SRA data (NCBImeta)
2. Download assemblies and SRA fastq files (sra-tools)
3. Build SnpEff database from reference (SnpEff)
4. Align to reference genome (snippy,eager)
5. Mask problematic regions (dustmasker, mummer, vcftools)
6. Evaluate statistics (qualimap, multiqc)
7. Construct a Maximum Likelihood phylogeny (iqtree)
8. Optimize time-scaled phylogeny (augur, treetime)
9. Web-based narrative visualization (auspice)

Showcase

• Presenting “The Plague”: Digital Exhibits as Interdisciplinary Method.
  DHSI Conference and Colloquium. June 5, 2020.
  Katherine Eaton, Nukhet Varlik, Ann Carmichael, Brian Golding, Hendrik Poinar.
  Digital Exhibit • Talk

• Plagues of the Past and Present.
  Lewis & Ruth Sherman Centre for Digital Scholarship. June 2, 2020.
  Katherine Eaton
  Digital Exhibit • Blog Post 1 • Blog Post 2 *

Install

All install options start by cloning the pipeline repo.

git clone https://github.com/ktmeaton/plague-phylogeography.git
cd plague-phylogeography

1. Conda (Laptop)

conda install -c conda-forge mamba
mamba env create -f workflow/envs/merge/environment.yaml
conda activate plague-phylogeography
snakemake --profile profiles/laptop help

(While mamba is not strictly necessary, it is heavily recommended.)

2. Docker (Laptop)

docker pull ktmeaton/plague-phylogeography:dev
docker run \
  -v $PWD:/pipeline \
  -w /pipeline \
  ktmeaton/plague-phylogeography:dev \
  snakemake --profile profiles/laptop help

3. Singularity (HPC - Compute Canada)

singularity pull docker://docker.io/ktmeaton/plague-phylogeography:dev
singularity exec plague_phylogeography_dev.sif \
  snakemake --profile profiles/compute-canada help

If you will be downloading data from the SRA with singularity, the sra toolkit must be configured:

mkdir -p ~/.ncbi/
printf '/LIBS/GUID = "%s"\n' `uuidgen` > ~/.ncbi/user-settings.mkfg;

Credits

Author: Katherine Eaton
Logo: Emil Karpinski, Katherine Eaton