GenPipes User Guide
GenPipes is an open source, next generation sequencing framework written in Python. Developed at the Canadian Centre for Computational Genomics (C3G), GenPipes facilitates writing and execution of multi-step genomics processing pipelines on HPC clusters. It offers 12 validated pipelines that include CoV, Tumor Pair, RNA, ChIP, DNA, Methylation and Hi-C sequencing.
Getting started
New users can quickly get started by referring to the Quick Start Guide. The seasoned users can directly jump into the Pipeline Reference Guide.
The latest GenPipes Version is 4.5.0. Refer to the release notes for more information regarding what is new, which pipelines were updated and what issues are fixed in this release.
To contribute, see Getting involved.
Happy genomic analysis with GenPipes!
Guides
- Release Notes
- GenPipes Quick Start Guide
- Pipelines Reference Guide
- Amplicon Sequencing Pipeline
- ChIP Sequencing Pipeline
- CoV Sequencing Pipeline
- DNA Sequencing Pipeline
- DNA Sequencing (High Coverage) Pipeline
- EpiQC Pipeline
- HiC Sequencing Pipeline
- Methylation Sequencing Pipeline
- Nanopore Pipeline
- Nanopore CoVSeQ Pipeline
- RNA Sequencing Pipeline
- De-Novo RNA Sequencing Pipeline
- RNA Sequencing (Light) Pipeline
- Tumor Pair Sequencing Pipeline
- Getting Involved