SnakeNgs (v0.4.0)

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

Warning

ngsFetch has been deprecated. Please use ngsfetch instead to fetch metadata and fastq files.

• RNA-seq
  • preprocessing_RNAseq.smk
  • rMATS.smk
  • SUPPA2_diffSplice.smk
  • Whippet.smk
  • MAJIQ.smk
  • LeafCutter.smk
• snRNA-seq
  • kb-nac.smk
  • STARsolo.smk
  • cellranger_count.smk
• ChIP-seq
  • preprocessing_ChIPseq.smk
  • callpeak_ChIPseq.smk
• ATAC-seq
  • callpeak_ATACseq.smk
  • differential_ATACseq.smk
  • footprinting_ATACseq.smk
  • footprinting_timeseries_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.

Contributing

Thank you for wanting to improve SnakeNgs! If you have any bugs or questions, feel free to open an issue or pull request.

Authors

• Naoto Kubota (0000-0003-0612-2300)