GenPipes is an open source Python-based Workflow Management System (WMS) for Next Generation Sequencing (NGS) genomics pipeline development.

As part of its implementation, GenPipes includes a set of high-quality, standardized analysis pipelines, designed for high-performance computing (HPC) resources and cloud environments.

GenPipes pipelines have been tested, continuously improved through industry standard benchmarks, and used extensively since its first release in 2013. By combining both WMS and extensively validated end-to-end genomic analysis workflows, into a simple tool, GenPipes not only enables bioinformatics professionals but also students, researchers in need of bioinformatics tools to perform turnkey analyses for a wide range of bioinformatics applications in the genomics field. It also allows flexible and robust extensions for advanced genomics research.

You can learn more about GenPipes, its target audience, sponsors, how the project has evolved over the years and license information in the following section.

Release Notes

You can refer to the detailed list of changes for past and current releases of GenPipes through the Release Notes.

Getting Help

GenPipes is under active development. If you need help, would like to contribute, or simply want to talk about the project with the team members, we have a number of open channels for communication.

To report bugs or file feature requests: use the GenPipes issue tracker. For details, see the GenPipes Support Page.

To talk about the project with people in real time: join the GenPipes Channel on Google Groups. For more details refer to the Channels page.

To contribute code or documentation changes: submit a pull request on GenPipes BitBucket.

For citations, publications, workshops,test data sets and other resources, visit Resources page.