GenPipes: an open-source framework for distributed and scalable genomic analyses
| Autor: | Marc Michaud, Eloi Mercier, Mathieu Bourgey, Pierre-Olivier Quirion, Gary Leveque, Johanna Sandoval, Maxime Caron, Emmanuel Gonzalez, Joel Fillon, Julien Tremblay, Guillaume Bourque, Francois Lefebvre, Louis Letourneau, Patrick Tran Van, David Anderson de Lima Morais, Rola Dali, Xiaojian Shao, Edouard Henrion, Robert Eveleigh, B. Caron, Pascale Marquis, Kuang Chung Chen, David Bujold |
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| Rok vydání: | 2018 |
| Předmět: |
0106 biological sciences
Epigenomics Computer science workflow 0206 medical engineering Health Informatics Cloud computing Genomics 02 engineering and technology 01 natural sciences DNA sequencing 03 medical and health sciences bioinformatics frameworks genomics pipeline workflow management systems Server Technical Note Humans computer.programming_language 030304 developmental biology 0303 health sciences business.industry Sequence Analysis RNA Sequence Analysis DNA Python (programming language) DNA Methylation Computer Science Applications Workflow Metagenomics Scalability Software engineering business computer 020602 bioinformatics Software 010606 plant biology & botany |
| Zdroj: | GigaScience GigaScience, vol. 8, no. 6 |
| ISSN: | 2047-217X |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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