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SnakeNgs documentation

Pipelines for NGS data analysis written in Snakemake. Each pipeline is designed to be executed with Singularity containers.

Quick start

  1. Make sure you have Singularity and Snakemake installed.

  2. Clone the repository and run the pipeline of your choice (e.g., preprocessing_RNAseq.smk).

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# Clone the repository
git clone https://github.com/NaotoKubota/SnakeNgs.git

# Run the pipeline
snakemake -s /path/to/SnakeNgs/snakefile/preprocessing_RNAseq.smk \
--configfile /path/to/config.yaml \
--cores 16 \
--use-singularity \
--rerun-incomplete

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