Available Pipelines

Genomic Analysis	Pipeline	Flag	More Information
ChIP-Seq	chipseq.py		ChIP-Seq Manual
RNA-Seq	rnaseq.py		RNA-Seq Manual
De novo RNA-Seq	rnaseq_denovo_assembly.py		RNA-Seq De Novo Manual
Whole Genome Seq	dnaseq.py	default	Whole Genome Seq Manual
Exome Seq	dnaseq.py	capture BED file in Readset file or init file	Exome Seq Manual
Deep Whole Genome	dnaseq.py	default	DNA High Coverage Seq Manual
Deep Exome Seq	dnaseq_high_coverage.py	capture BED file in Readset file or init file	Deep Exome Seq Manual
Hi-C Seq	hicseq.py	-t hic	Hi-C Seq Manual
Capture Hi-C	hicseq.py	-t capture	Hi-C Capture Manual
Whole Genome Methyl Seq	methylseq.py	default	Methyl WGS Manual
Capture Methyl Seq	methylseq.py	capture BED file in Readset file or init file	Capture Methyl WGS Manual
Cancer Analysis	tumor_pair.py Note Deprecated As of GenPipes release 3.2.0 this pipeline is no longer available.		Cancer Analysis Manual
Meta Genomics	ampliconseq.py		Meta Genomics Manual
SARS-CoV-2	covseq.py		SARS-COV-2 Sequencing