README.md

SnakeNgs (v0.2.0)

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

Usage

1. Make sure you have Singularity and Snakemake installed.

2. Clone the repository.

git clone https://github.com/NaotoKubota/SnakeNgs.git

3. 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-incomplete

That's it! You can find the detailed usage of each pipeline in the documentation.

Workflow

• Fetching
  • ngsFetch
• RNA-seq
  • preprocessing_RNAseq.smk
  • preprocessing_RNAseq_single.smk
  • rMATS.smk
  • SUPPA2_diffSplice.smk
  • Whippet.smk
  • MAJIQ.smk
  • LeafCutter.smk
• snRNA-seq
  • kb-nac.smk
• ChIP-seq
  • preprocessing_ChIPseq.smk
  • preprocessing_ChIPseq_single.smk
  • callpeak_ChIPseq.smk
• ATAC-seq
  • callpeak_ATACseq.smk
  • differential_ATACseq.smk
  • footprinting_ATACseq.smk
• iCLIP-seq & HITSCLIP
  • preprocessing_iCLIPseq.smk
  • preprocessing_HITSCLIP.smk
• File format conversion
  • bam2cram.smk

Documentation

You can learn how to use each pipeline by visiting the documentation.