An easy breezy whole-genome derived snp-based phylogenetic pipeline 🌪️

Installation

Pre-requisites

1. Any kind of conda environment
   • anaconda, miniconda, micromamba
   • I recommend mamba
2. A git installation (optional)
3. Linux system

1. Clone this repository

Everything you'll need is right here in this repository, which will also be your project directory. You'll need to clone this repository for every new project (it's very lightweight). Feel free to rename the gust folder to whatever is relevant for your project.

with git (recommended)

git clone https://github.com/pdimens/gust.git

without git

wget -O gust.zip https://github.com/pdimens/gust/archive/refs/heads/main.zip
unzip gust.zip  # or whatever archive extractor you have

2. Initiate the gust conda environment

🌪️ if you already have a gust conda environment, skip this step 🌪️

Use the provided gust_env.yaml conda configuration file to create a new conda environment. If not using conda, replace conda with the appropriate environment framework, (mamba, micromamba, etc.)

cd gust   # enter the gust directory
conda env create -f .other/gust_env.yaml

This will create a new environment called gust containing all the software dependencies. Activate the environment with:

conda activate gust

Usage

Preparation

It's minimal, I swear.

1. Put all of the genomes you want included in analysis in the genomes folder
   • make sure the files end with .fasta
   • I haven't figured out how to make snakemake more flexible with this (PR's welcome!)
2. Specify the name of the reference genome and outgroup genome in config.yml
   • the genomes should be in the genomes/ folder
   • use just the name, not the full path
   • e.g. "bostauros.fasta" ✅ vs "genomes/bostauros.fasta" ❌
3. [optional] Modify software parameters in config.yml

Running

• activate the gust environment with conda activate gust

If you call gust without arguments you will see help text, otherwise:

./gust numThreads configFile

where numThreads is the number of threads to use (>1, no default) and configFile is the name of the configuration file (optional, defaults to config.yml).

examples

Running gust with 25 threads using the configuration file config.yml

./gust 25

Running gust with 10 threads using the configuration file frag250.yml

./gust 10 frag250.yml