Version history

Initial release of nf-core/hicar pipeline.


  • Raw read QC (FastQC)
  • Adapter trimming (cutadapt)
  • Map and filter reads (bwa_mem, samtools, pairtools)
  • Call peaks for ATAC (R2) reads (MACS2)
  • Find genomic interactions and annotations (MAPS, ChIPpeakAnno)
  • Differential analysis and annotations (edgeR, ChIPpeakAnno)
  • Alignment QC metrics (samtools)
  • ATAC R2 reads QC metrics (ATACseqQC)
  • Pair QC metrics (pairsqc)
  • Visualization (cooler, trackViewer, circos, ucsc_tools, bedtools, juicer_tools, igv.js)
  • Collate and present various QC metrics (MultiQC)