snakemake-workflows/chipseq ↗
Created Feb 22, 2021 · View the snakemake-workflows/chipseq repository page
ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).
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Contributors
2
Lines of Code
123
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Apr 15, 2020
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Oct 21, 2020
About snakemake-workflows/chipseq
This is a Snakemake workflow for ChIP-seq analysis, implementing a bioinformatics pipeline for chromatin immunoprecipitation sequencing experiments. The pipeline handles peak-calling, quality control, and differential analysis of ChIP-seq data. It represents a port of the nextflow pipeline from nf-co.re/chipseq into Snakemake, a workflow management system popular in computational biology.
The workflow is designed to be flexible and reproducible, allowing users to configure analysis parameters through YAML config files and sample sheets. It supports local execution across multiple cores as well as distributed computing on cluster environments using technologies like DRMAA or grid job schedulers. The pipeline integrates conda for environment management and Singularity for containerization, ensuring consistent software dependencies and reproducibility across different computing systems.
The project targets bioinformaticians and researchers performing ChIP-seq analyses. It includes testing infrastructure with continuous integration through GitHub Actions, and provides functionality to generate interactive HTML reports of analysis results. Users can easily synchronize their local copies with upstream updates and contribute improvements back to the original repository through standard GitHub workflows.
