Seabreeze

Author: Ira Zibbu

Last update to README: 2024-08-28

Seabreeze is an automated pipeline for structural variant analysis from bacterial resequencing experiments, and this repository holds the a version of seabreeze adapted to analyse structural variants

Seabreeze uses snakemake to neatly manage input/output file and conda environment dependencies.

Updates

As of August 2024, the general purpose structural variant analysis tool seabreeze is now hosted separately on the BarrickLab GitHub. Please use that version for your own data, and not this.

Quick start

To replicate analysis, follow these steps:

1. Clone this repository

git clone https://github.com/ira-zibbu/seabreeze.git

2. Create the seabreeze conda environment

 conda env create --name seabreeze --file bin/workflow/envs/seabreeze.yml

3. Create a folder for the conda environments

To allow Snakemake to keep reusing conda environments (i.e to prevent Snakemake from reinstalling environments again and again), do the following:

mkdir $HOME/snakemake_conda_envs

Add this line to your .bashrc .zshrc or whatever shell you are currently using:

export SNAKEMAKE_CONDA_PREFIX=$HOME/snakemake_conda_envs

4. Add test data

This is a small test data set to make sure everything runs okay

cp -r test data
cp data/data.csv ../data.csv

5. You're all set! Navigate to the seabreeze directory and run snakemake with a few magic words:

conda activate seabreeze
snakemake --use-conda --cores 4 # feel free to change this but anything less than 2 cores will probably take an hour 

Misc information

Where does seabreeze get its name from? Structural variant for bacterial resequencing abbreviates as SVbrese, which sounded like seabreeze.