GenPipes: an open-source framework for distributed and scalable genomic analyses
GenPipes: an open-source framework for distributed and scalable genomic analyses
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DOI：
10.1093/gigascience/giz037
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发表时间：
2019-06-01
期刊：
影响因子：
9.2
通讯作者：
Bourque, Guillaume
中科院分区：
文献类型：
--
作者：
Bourgey, Mathieu;Dali, Rola;Bourque, Guillaume
工作背景：随着测序成本的降低以及基因组学技术和方案的快速发展，对能够进行有效的大规模数据处理的经验证的生物信息学软件的需求正在增长。调查结果：在这里，我们介绍了GenPipes，一个灵活的基于Python的框架，可以促进针对高性能计算集群和云优化的多步骤工作流的开发和部署。GenPipes已经为各种基因组学应用实施了12个经过验证和可扩展的管道，包括RNA测序、染色质免疫沉淀测序、DNA测序、甲基化测序、Hi-C、捕获Hi-C、宏基因组学和Pacific Biosciences长读组装。该软件在GPLv 3开源许可下提供，并不断更新以跟踪基因组学和生物信息学的最新进展。该框架已经在多个服务器上配置，并且还提供了Docker镜像以方便其他安装。结论：GenPipes为基因组学研究人员提供了一种简单的方法来分析不同类型的数据，可根据他们的需求和资源进行定制，以及创建自己的工作流程的灵活性。
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.