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. Align assemblies and fastq files to a reference genome.
   • snippy
   • nf-core/eager
4. Mask problematic regions.
   • dustmasker
   • mummer
   • vctools
5. Evaluate statistics.
   • qualimap
   • multiqc
6. Estimate a maximum-likelihood phylogeny.
   • iqtree
7. Estimate a time-scaled phylogeny.
   • lsd2
8. Web-based 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

• Create a conda environment with dependencies.
• Mamba is not strictly necessary but it is heavily recommended.

conda install -c conda-forge mamba
mamba env create -f workflow/envs/merge/environment.yaml

• Install LSD2 (not available through conda).

# Download binary
wget https://github.com/tothuhien/lsd2/releases/download/v1.9.9/lsd2_unix
# Move into the conda binary path and rename
mv lsd2_unix ~/miniconda3/envs/plague-phylogeography/bin/lsd2

• Test the help command.

snakemake --profile profiles/laptop help

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

snakemake --profile profiles/laptop all

2. Docker

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

Demo

1. Conda

snakemake --profile profiles/laptop all

2. Docker

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

Credits

Author: Katherine Eaton
Logo: Emil Karpinski, Katherine Eaton