Available Pipelines

Genomic Analysis	genpipes <command_name>	Protocol Options
ChIP Sequencing	chipseq	None
RNA Sequencing	rnaseq	-t chipseq (default) or -t atacseq
RNA Sequencing Light	rnaseq_light	None
Denovo RNA Sequencing	rnaseq_denovo_assembly	-t trinity (default) or -t seq2fun
Whole Genome Sequencing	dnaseq	-t germline_snv (default) or -t germline_sv
Exome Sequencing	dnaseq	capture BED file in Readset file or ini file
Deep Whole Genome Sequencing	dnaseq	use relevant ini file and -t germline_high_cov
Deep Exome Sequencing	dnaseq	capture BED file in Readset file or ini file
Whole Genome Methyl Sequencing	methylseq	bismark (default) or -t gembs or -t hybrid or -t dragen or
Capture Methyl Sequencing	methylseq	capture BED file in Readset file or ini file
Cancer Analysis	dnaseq	-t somatic_ensemble or -t somatic_sv or -t somatic_fastpass or -t somatic_tumor_only
Long-Reads Whole Genome Sequencing	longread_dnaseq	-t nanopore or -t nanopore_paired_somatic or -t revio (Note -t nanopore_paired_somatic option also requires -p pair_file_name)
Meta Genomics	ampliconseq	None
SARS-COV-2 Analysis	covseq	None