GenPipes: an open-source framework for distributed and scalable genomic analyses

Bourgey, M.; Dali, R.; Eveleigh, R.; Chen, K. C.; Letourneau, L.; Fillon, J.; Michaud, M.; Caron, M.; Sandoval, J.; Lefebvre, F.; Leveque, G.; Mercier, E.; Bujold, D.; Marquis, P.; Tran Van, P.; Morais, D.; Tremblay, J.; Shao, X.; Henrion, E.; Gonzalez, E.; Quirion, P.-O.; Caron, B.; Bourque, G.

doi:10.1101/459552

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bioRxiv · 10.1101/459552

GenPipes: an open-source framework for distributed and scalable genomic analyses

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Abstract

With the decreasing cost of sequencing and the rapid developments in genomics technologies and protocols, the need for validated bioinformatics software that enables efficient large-scale data processing is growing. Here we present GenPipes, a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for High Performance Computing clusters and the cloud. GenPipes already implements 12 validated and scalable pipelines for various genomics applications, including RNA-Seq, ChIP-Seq, DNA-Seq, Methyl-Seq, Hi-C, capture Hi-C, metagenomics and PacBio long read assembly. The software is available under a GPLv3 open source license and is continuously updated to follow recent advances in genomics and bioinformatics. The framework has been already configured on several servers and a docker image is also available to facilitate additional installations. In summary, GenPipes offers genomic researchers a simple method to analyze different types of data, customizable to their needs and resources, as well as the flexibility to create their own workflows.

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Bourgey, M., Dali, R., Eveleigh, R., Chen, K. C., Letourneau, L., Fillon, J., Michaud, M., Caron, M., Sandoval, J., Lefebvre, F., Leveque, G., Mercier, E., Bujold, D., Marquis, P., Tran Van, P., Morais, D., Tremblay, J., Shao, X., Henrion, E., Gonzalez, E., Quirion, P.-O., Caron, B., Bourque, G.. 2018-11-01. GenPipes: an open-source framework for distributed and scalable genomic analyses. https://doi.org/10.1101/459552

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