snakePipes

snakePipes provides Snakemake-based, scalable workflows for analysis of next-generation sequencing (NGS) epigenomic assays including ChIP-seq, RNA-seq, Bisulfite-seq, ATAC-seq, Hi-C, and single-cell RNA-seq to support studies of gene regulation, chromatin accessibility, DNA methylation, and 3D genome organization.

Key Features:

• Modular Workflow Design: Supports analysis workflows for ChIP-seq, RNA-seq, Bisulfite-seq, ATAC-seq, Hi-C, and single-cell RNA-seq.
• Snakemake-based Execution: Implements workflows using Snakemake for rule-based, reproducible execution.
• Scalability: Capable of processing large NGS datasets suitable for both small-scale and high-throughput studies.
• Workflow Configurability: Allows configuration of processing steps and parameters via YAML configuration files.
• Integration of Bioinformatics Tools: Assembles and integrates multiple bioinformatics tools within workflows for epigenomic analyses.

Scientific Applications:

• Gene regulation: Analysis of gene regulation using ChIP-seq and RNA-seq datasets.
• Chromatin accessibility: Analysis of chromatin accessibility from ATAC-seq data.
• DNA methylation patterns: Analysis of DNA methylation using Bisulfite-seq data.
• 3D genome organization: Analysis of three-dimensional genome organization using Hi-C data.

Methodology:

Workflows are assembled and integrated from multiple bioinformatics tools, executed using Snakemake, and configured through YAML files that define processing steps and parameters.