nf-core/epigenomesegmentation
nf-core/epigenomesegmentation is a reproducible Nextflow pipeline for running chromatin and epigenome segmentation analyses using EpiSegMix and EpiSegMixMeth.
Rather than providing a new segmentation algorithm itself, the pipeline organizes the complete computational workflow around these methods. It standardizes input handling, execution, software dependencies, and output generation and can be run reproducibly on local systems, HPC clusters, and cloud infrastructure.
Built according to nf-core community standards, the pipeline uses containerized and version-controlled software environments and supports established deployment technologies such as Docker, Singularity/Apptainer, and Conda.
Key Benefits
Reproducible execution of EpiSegMix and EpiSegMixMeth analyses
Standardized workflow for epigenome segmentation
Portable across local, HPC, and cloud environments
Containerized and version-controlled software dependencies
Integration into established nf-core and Nextflow infrastructures
Applications
Running genome-wide chromatin state segmentation workflows
Reproducible analysis of histone ChIP-seq, DNA methylation, and open-chromatin data
Standardized execution across research groups and computing environments
Scaling epigenome segmentation analyses to larger datasets
Integration into automated and reproducible bioinformatics workflows
Intended Use
nf-core/epigenomesegmentation is intended for researchers who want to run EpiSegMix/EpiSegMixMeth in a standardized, reproducible workflow without manually setting up the complete software environment and computational pipeline.
Contact:
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