hicar - 1.0.0

Initial release of nf-core/hicar pipeline.

Added

• 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, ucsctools, bedtools, juicertools, igv.js)
• Collate and present various QC metrics (MultiQC)

- Nextflow
Published by jianhong about 4 years ago