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Assay
2
ATAC-seq
1
DNase-seq
Pipeline status
3
active
Pipeline groups
1
ATAC-seq Pipeline (ENCODE replicated)
1
ATAC-seq Pipeline (ENCODE unreplicated)
1
DNase-seq Pipeline (ENCODE)
Software
3
Picard
3
Samtools
3
bedToBigBed
3
cutadapt
2
BEDTools
2
Bowtie 2
2
Irreproducible Discovery Rate (IDR)
2
MACS2
2
overlap_peaks.py
2
sambamba
1
BEDOPS
1
BWA
1
Digital genomic footprinting
1
Phantompeakqualtools
1
hotspot2
Developed by
3
AMP-T2D consortium
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BWA
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Pipeline
DPL930NXT
active
DNase-seq Pipeline (ENCODE)
Assays:
DNase-seq
Software:
hotspot2, BEDOPS, BWA, cutadapt, Samtools, Picard, Digital genomic footprinting, bedToBigBed
Pipeline
DPL707AXE
active
ATAC-seq Pipeline (ENCODE replicated)
Assays:
ATAC-seq
Software:
Bowtie 2, Samtools, Picard, cutadapt, sambamba, overlap_peaks.py, bedToBigBed, Irreproducible Discovery Rate (IDR), BEDTools, MACS2, Phantompeakqualtools
Pipeline
DPL967MZM
active
ATAC-seq Pipeline (ENCODE unreplicated)
Assays:
ATAC-seq
Software:
Bowtie 2, Samtools, Picard, cutadapt, sambamba, Irreproducible Discovery Rate (IDR), overlap_peaks.py, MACS2, BEDTools, bedToBigBed