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

NRC publication: Yes

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Bibliographic Details
Published in:Gigascience Vol. 8; no. 6
Main Authors: Bourgey, Mathieu, Dali, Rola, Eveleigh, Robert, Chen, Kuang Chung, Letourneau, Louis, Fillon, Joel, Michaud, Marc, Caron, Maxime, Sandoval, Johanna, Lefebvre, Francois, Leveque, Gary, Mercier, Eloi, Bujold, David, Marquis, Pascale, Van, Patrick Tran, Anderson de Lima Morais, David, Tremblay, Julien, Shao, Xiaojian, Henrion, Edouard, Gonzalez, Emmanuel, Quirion, Pierre-Olivier, Caron, Bryan, Bourque, Guillaume
Format: Journal Article
Language:English
Published: United States Oxford University Press 01.06.2019
Subjects:
Bioinformatics
Chromatin
Cost analysis
Data processing
DNA Methylation
DNA sequencing
Epigenomics - methods
frameworks
Gene sequencing
Genomic analysis
Genomics
Genomics - methods
Humans
Immunoprecipitation
Metagenomics
Metagenomics - methods
Open source software
pipeline
Pipelining (computers)
Sequence Analysis, DNA - methods
Sequence Analysis, RNA - methods
Software
Technical Note
workflow
workflow management systems
workflow management systems
pipeline
genomics
workflow
frameworks
bioinformatics
ISSN:2047-217X, 2047-217X
Online Access:Get full text
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Description
Summary:NRC publication: Yes
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.
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ISSN:2047-217X
2047-217X
DOI:10.1093/gigascience/giz037