Pipelines for NGS data analysis written in Snakemake. Each pipeline is designed to be executed with Singularity containers.
-
Make sure you have Singularity and Snakemake installed.
-
Clone the repository.
git clone https://github.com/NaotoKubota/SnakeNgs.git- Run the pipeline of your choice (e.g.,
preprocessing_RNAseq.smk).
snakemake -s /path/to/SnakeNgs/snakefile/preprocessing_RNAseq.smk \
--configfile /path/to/config.yaml \
--cores 16 \
--use-singularity \
--rerun-incompleteThat's it! You can find the detailed usage of each pipeline in the documentation.
- Fetching
- RNA-seq
- snRNA-seq
- ChIP-seq
- ATAC-seq
- iCLIP-seq & HITSCLIP
- File format conversion
You can learn how to use each pipeline by visiting the documentation.