GenPipes User Guide¶
GenPipes is an open source framework developed at Canadian Centre for Computational Genomics (C3G) to facilitate writing and execution of multi-step processing pipelines on HPC clusters. GenPipes is written in Python and is primarily geared towards Next Generation Sequencing analysis. It comes with 12 validated pipelines that include RNA-Seq, ChIP-Seq, DNA-Seq, Methyl-Seq and Hi-C processing.
The new users can get started by referring to the Quick Start Guide. Seasoned users can refer to specifics of any of the pipelines by browsing the Pipeline Reference section.
Users can refer to latest release notes for GenPipes Version 4.4.0 for more information regarding what is new, which pipelines were updated and what issues are fixed in this release.
If you wish to not only use GenPipes Open Source offering but also contribute to the same or contribute to GenPipes documentation, refer to the section Getting involved below.
Happy genomic analysis with GenPipes!
This GenPipes User Guide is organized as follows:
- 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
- Latest GenPipes Release Note
- Get Involved with GenPipes