GitHub - CCBR/Pipeliner: An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.

Welcome to Pipeliner - an open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.

Pipeliner provides access to a set of best-practices NGS pipelines developed, tested, and benchmarked by experts at CCBR and NCBR.

Questions or need help?

Please check out our FAQ or contact page for different ways of getting in touch with the team.

Pipeliner is CHANGING!!!

Please visit CCBR github page for new features and release schedule.

Name		Name	Last commit message	Last commit date
Latest commit History 1,559 Commits
Data		Data
Manpages		Manpages
References		References
Reporter		Reporter
Results-template		Results-template
Rules		Rules
gui		gui
.gitattributes		.gitattributes
.gitignore		.gitignore
GRCh38.json		GRCh38.json
Mmul_8.0.1.json		Mmul_8.0.1.json
PipelinerOverview.pdf		PipelinerOverview.pdf
README.md		README.md
RNASeqDocumentation.pdf		RNASeqDocumentation.pdf
canFam3.json		canFam3.json
ccbrpipe.sh		ccbrpipe.sh
cluster.debug.json		cluster.debug.json
cluster.json		cluster.json
cluster.non-debug.json		cluster.non-debug.json
contrasts.tab		contrasts.tab
hg19.json		hg19.json
hg38.json		hg38.json
hg38_30.json		hg38_30.json
hg38_30_KSHV.json		hg38_30_KSHV.json
hg38_HPV16.json		hg38_HPV16.json
hs37d5.json		hs37d5.json
hs38d1.json		hs38d1.json
makeasnake.py		makeasnake.py
mkdocs.yml		mkdocs.yml
mm10.json		mm10.json
mm10_M21.json		mm10_M21.json
mm10_M25.json		mm10_M25.json
mm10_M29.json		mm10_M29.json
mm9.json		mm9.json
oldpipe.sh		oldpipe.sh
oldwiki.md		oldwiki.md
pairs		pairs
pipeline_ctrl.sh		pipeline_ctrl.sh
pipeliner-logo.bmp		pipeliner-logo.bmp
pipeliner-logo.gif		pipeliner-logo.gif
pipeliner-rwb.json		pipeliner-rwb.json
pipeliner.json		pipeliner.json
pipeliner.manual		pipeliner.manual
pipeliner.py		pipeliner.py
pipeliner2.py		pipeliner2.py
project.json		project.json
rg.tab		rg.tab
rules.json		rules.json
run_spp.R		run_spp.R
samples		samples
slurm.template		slurm.template
snakefile.template		snakefile.template
standard-bin.json		standard-bin.json
submit_slurm.template		submit_slurm.template
symfiles.pl		symfiles.pl