yEvo Pipeline

Variant calling Snakemake pipeline for analyzing yEvo sequencing data.

Installation

1. Make sure you have conda installed.

2. Install Mamba to facilitate snakemake installation, as recommended in the Snakemake docs.

$ conda install -n base -c conda-forge mamba

3. Clone this repo:

$ git clone https://github.com/dunhamlab/yevo_pipeline.git

4. Create the provided environment using Mamba:

$ cd yevo_pipeline/ && mamba env create -f environment.yml

5. Activate the new conda environment:

$ conda activate yevo_pipeline_env

6. Download the required pipeline inputs and test sequencing data:

$ ./scripts/download_test_data.sh

7. Generate the run_pipeline.sh script using the included utility script:

$ ./scripts/gen_run_script.sh

You're ready to run the pipeline!

Running the Pipeline

After following the above installation instructions, run the pipeline on the provided test input files:

$ ./run_pipeline.sh

NOTE: be sure that you are in the repo's base directory with the yevo_pipeline_env conda environment activated.

To run this pipeline on your own sequencing data, configure runs using run_pipeline.sh:

• FASTQ_DIR is the absolute path to the raw data (e.g. fastq.gz) directory
• OUTPUT_DIR is the absolute path to your desired output directory, which Snakemake will create

Reference genome, ancestor, and annotation file paths are located in the config/config.yml file and can also be modified as needed.