Take a closer look at one of C3G’s software tools; its purpose, its strengths, its newest features, and how it continues to support the life science community.
What is GenPipes?
GenPipes pipelines provide high-quality genomic analyses optimized for high-performance computing (HPC) and cloud environments. It is an open-source (LGPL), Python-based platform for managing -omics workflows. GenPipes is widely adopted across the life sciences, serving bioinformatics professionals, students, and researchers working on a broad range of genomic analyses and has extensive documentation explaining each pipeline and its outputs to users.
What sets GenPipes apart from other analysis platforms or workflow management systems?
GenPipes stands out for its flexibility, scalability, and ease of use. It adapts quickly to new systems, supports multiple job schedulers and deployment types, and includes a broad set of ready-to-use pipelines. Its integration with the Digital Research Alliance of Canada makes it particularly appealing to Canadian researchers, offering a pre-installed solution for several standard–omics analyses.
GenPipes also has a low barrier to entry; users don’t need to install software, manage reference genomes, or configure compute resources, allowing them to start their analyses quickly and confidently!
What are the most used pipelines in GenPipes?
The most widely used pipelines in GenPipes are ChIP‑Seq, RNA‑Seq, and DNA‑Seq. The DNA‑Seq pipeline supports multiple protocols, making it suitable for both standard whole‑genome analyses and paired cancer genomics workflows. The pipelines output multiple reports and standard files, such as BAM, VCFs, peak-calls and expression matrices.
Does GenPipes have any features to help students and early-career researchers?
Yes! To make GenPipes even more accessible to new users, we developed a new tool called the GenPipes Wizard, with the help of an excellent C3G intern, Alexa Li Kim Wa.
The Wizard is an interactive assistant that helps users:
- Quickly identify the pipeline best suited to their data
- Automatically generate the correct command to launch their analysis
What is the most recent version of GenPipes?
We continuously enhance GenPipes based on user feedback and internal benchmarking. Last year’s major release was v.6.1.0, which introduced new pipelines and streamlined the interface by retiring tools that are no longer in use.
Our latest release is a minor update, focused on fixing small bugs uncovered through testing or reported by users. Click the link to learn more about our latest version: v.6.1.1.
If you’d like to help shape future improvements, we encourage users to email us:
pipelines@computationalgenomics.ca
*Users should be aware of whether a release is major, medium, or minor. Major releases may break backward compatibility, which is important for long-running projects that require comparable results. All previous GenPipes versions remain available as modules, so analyses can always be repeated with an older version if needed*
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