Container-based bioinformatics with Pachyderm

← Back to publications

Published: 2019-03-04

Formatted citation

Novella JA, Khoonsari PE, Herman S, Whitenack D, Capuccini M, Burman J, Kultima K, Spjuth O. Container-based bioinformatics with Pachyderm.
Bioinformatics. 35, 5, 839-846. (2019). DOI: 10.1093/bioinformatics/bty699


Motivation: Computational biologists face many challenges related to data size, and they need to manage complicated analyses often including multiple stages and multiple tools, all of which must be deployed to modern infrastructures. To address these challenges and maintain reproducibility of results, researchers need (i) a reliable way to run processing stages in any computational environment, (ii) a well-defined way to orchestrate those processing stages, and (iii) a data management layer that tracks data as it moves through the processing pipeline. Results: Pachyderm is an open-source workflow system and data management framework that fulfills these needs by creating a data pipelining and data versioning layer on top of projects from the container ecosystem, having Kubernetes as the backbone for container orchestration. We adapted Pachyderm and demonstrated its attractive properties in bioinformatics. A Helm Chart was created so that researchers can use Pachyderm in multiple scenarios. The Pachyderm File System was extended to support block storage. A wrapper for initiating Pachyderm on cloud-agnostic virtual infrastructures was created. The benefits of Pachyderm are illustrated via a large metabolomics workflow, demonstrating that Pachyderm enables efficient and sustainable data science workflows while maintaining reproducibility and scalability. Availability: Pachyderm is available from The Pachyderm Helm Chart is available from Pachyderm is available out-of-the-box from the PhenoMeNal VRE ( and general Kubernetes environments instantiated via KubeNow. The code of the workflow used for the analysis is available on GitHub (