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Nextflow ChIP-seq data analysis pipeline, National Genomics Infrastructure, Science for Life Laboratory in Stockholm
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Build Status Nextflow

This pipeline has moved

This pipeline has been moved to the new nf-core GitHub organisation. You can now find it here:

This repository will be archived to maintain the release version for future reproducability, to allow reruns.

If you have any questions, please get in touch:

// Phil Ewels, 2018-04-24


NGI-ChIPseq is a bioinformatics best-practice analysis pipeline used for ChIP-seq (chromatin immunoprecipitation sequencing) data analysis at the National Genomics Infastructure at SciLifeLab Stockholm, Sweden.

The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.

This pipeline is primarily used with a SLURM cluster on the Swedish UPPMAX systems. However, the pipeline should be able to run on any system that Nextflow supports. We have done some limited testing using Docker and AWS, and the pipeline comes with some configuration for these systems. See the installation docs for more information.


The NGI-ChIPseq pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation and configuration
  2. Running the pipeline
  3. Output and how to interpret the results

If you're interested in running the pipeline in the cloud, please read the docs about using our pipeline with Amazon Web Services on the NGI-ChIPseq pipeline (the instructions should work with this pipeline as well).


These scripts were written for use at the National Genomics Infrastructure at SciLifeLab in Stockholm, Sweden. Written by Chuan Wang (@chuan-wang) and Phil Ewels (@ewels).

SciLifeLab National Genomics Infrastructure