GenPipes: an open-source framework for distributed and scalable genomic analyses
Gigascience, 2019•academic.oup.com
Background 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. Findings 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 technologies and protocols, the need for validated bioinformatics software that
enables efficient large-scale data processing is growing. Findings 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 …
Background
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.
Findings
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 sequencing, chromatin immunoprecipitation sequencing, DNA sequencing, methylation sequencing, Hi-C, capture Hi-C, metagenomics, and Pacific Biosciences 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 already been configured on several servers, and a Docker image is also available to facilitate additional installations.
Conclusions
GenPipes offers genomics 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.
Oxford University Press