Table 2 4D Nucleome analysis pipelines.

Pipeline	Steps	Software	Available file formats	CWL/WDL filename
Hi-C¹	Alignment	bwa-mem	.bam	bwa-mem.cwl
	Filtering	pairtools	.pairs	hi-c-processing-bam.cwl
	Merging replicates & matrix aggregation	cooler	.hic, .mcool	hi-c-processing-pairs.cwl
MARGI²	Alignment	bwa-mem	.bam	imargi-processing-fastq.cwl
	Filtering	pairtools	.pairs	imargi-processing-bam.cwl
	Merging replicates & matrix aggregation	cooler	.mcool	imargi-processing-pairs.cwl
Repli-seq³	Alignment	bwa-mem	.bam	repliseq-parta.cwl
	Filtering	samtools	-
	Binning & aggregation	bedtools	.bw, .bg
CUT&RUN⁴	Alignment & filtering	bowtie2, Picard, samtools, bedtools	.bam, .bedpe	cut-and-run-processing.cwl
	Peak calling	SEACR	.bw, .bg, .bed	cut-and-run-postaln.cwl
ATAC-seq⁵	Alignment & filtering	bowtie2, bedtools	.bed	atac.wdl
	Peak calling	MACS2	.bw, .bigbed
ChIP-seq⁶	Alignment & filtering	bwa, bedtools	.bed	chip.wdl
	Peak calling	MACS2, SPP	.bw, .bigbed
RNA-seq⁷	Alignment	STAR	.bam	rna-seq-pipeline.wdl
	Expression quantification	RSEM	.tsv
	Read coverage	STAR	.bw

Listed below are (i) subdirectories for Docker images from https://hub.docker.com/r/4dndcic; (ii) subdirectories from github repositories at https://github.com/4dn-dcic/ that hold the CWL or WDL pipeline files; and (iii) subdirectories for more information from https://data.4dnucleome.org/resources/data-analysis/. Note that for the Repliseq pipeline as well as the WDL pipelines from ENCODE, there is only one workflow file for the whole pipeline.
¹4dn-hic, docker-4dn-hic/tree/v43/cwl, hi_c-processing-pipeline.
²imargi, iMARGI-Docker/tree/v1.1.1_dcic_4/src/cwl, imargi-pipeline.
³repliseq, docker-4dn-repliseq/tree/v16/cwl, repli-seq-processing-pipeline.
⁴cut-and-run-pipeline, docker-4dn-cut-and-run-pipeline/tree/v1/cwl, cut-and-run-pipeline.
⁵encode-atacseq, atac-seq-pipeline, atacseq-processing-pipeline.
⁶encode-chipseq, chip-seq-pipeline2, chipseq-processing-pipeline.
⁷encode-rnaseq, rna-seq-pipeline, rnaseq-processing-pipeline information.

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