Chromatin immunoprecipitation (ChIP-seq) analysis using BWA and MACS2 with QC steps.
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Build Status Nextflow Gitter

install with bioconda Docker Container available


nf-core/chipseq is a bioinformatics best-practice analysis pipeline used for chromatin immunoprecipitation (ChIP-seq) data analysis.

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.

Pipeline Steps

  • Make BWA reference genome index (optional)
  • FastQC
  • TrimGalore!
  • Align with BWA
  • Samtools sort, index, stats & convert to BED
  • Samtools idxstats
  • Picard MarkDuplicates
  • Count read statistics
  • PhantomPeakQualTools
  • SPP: Calculate NSCRSC and cross correlation
  • DeepTools bamPEFragmentSize, plotFingerprint, bamCoverage, multiBamSummary, plotCorrelation, plotPCA
  • NGSplot
  • MACS2 peak calling
  • Saturation analysis
  • ChIP peak annotation
  • MultiQC


The nf-core/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


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).