NGSeasy: a next generation sequencing pipeline in Docker containers
NGSeasy: a next generation sequencing pipeline in Docker containers
复制标题
NGSeasy：Docker 容器中的下一代测序管道
DOI：
--
复制
发表时间：
2015
期刊：
影响因子：
--
通讯作者：
S. Newhouse
中科院分区：
文献类型：
--
作者：
A. Folarin;R. Dobson;S. Newhouse
动机：生物信息管道经常使用大量组件，部署这些组件会招致巨大的配置和维护负担，这仍然是可重复研究的重大障碍。我们的目标是定义一种新的模式和最佳实践，用于开发、分发和运行封装在Docker Containers(轻量级虚拟化)中的管道，重点是下一代排序(NGS)工作流。这种方法提供了几个优点，即：效率、可移植性、版本化和可重复性。使用NGSasy管道，用户可以在任何环境(例如操作系统、工作站、集群、云)中快速部署任何管道版本。虽然这也可能通过虚拟机(VM)来实现；但VM缺乏可移植性，具有相当大的开销(磁盘、CPU、RAM)，并且需要静态配置分配的资源-Docker在很大程度上解决了这些问题。结果：我们使用一组版本化、模块化和可重用的容器构建块演示了为NGS打包和执行多组件管道的最佳实践。我们为Docker Containers中的下一代测序管道提供了一个基本的“概念验证”评估方案，能够产生与公共和“最佳实践”工作流相媲美的有意义的结果，而且对标准计算性能几乎没有影响。可用性：每个组件的版本化Dockerfile和容器镜像都分别在GitHub和Docker Hub上发布。管道和容器可以从Docker Hub拉出，并在任何能够运行Docker平台的环境中执行，运行NGS管道的硬件要求最低。
Motivation : Bioinformatic pipelines often use large numbers of components and deploying them incurs substantial configuration and maintenance burden that remains a significant barrier to reproducible research. Our aim is to define a new paradigm and best practices for developing, distributing and running pipelines encapsulated in Docker containers (lightweight virtualization), with a focus on next generation sequencing (NGS) workflows. This approach provides several advantages, namely: efficiency, portability, versioning and reproducibility. Using the NGSeasy pipeline, a user can quickly deploy any pipeline version in any environment (e.g. operating systems, workstations, clusters, clouds). While this might also be achieved with a virtual machine (VM); VMs lack portability, have substantial overhead (disk, CPU, RAM), and require allocated resources to be provisioned statically – Docker, to a large extent, solves these issues. Results : We demonstrate best practices for packaging and execution of a multicomponent pipeline for NGS using a set of container building blocks which are versioned, modular and reusable. We present a basic ”proof of concept” evaluation of a next generation sequencing pipeline in Docker containers, capable of producing meaningful results, that are comparable with public and ”best practice” workflows, with little to no impact on standard computing performance. Availability : Both versioned Dockerfiles and container images for each component are published on GitHub and Docker Hub, respectively. The pipeline and containers can be pulled from Docker Hub and executed on any environment capable of running the Docker platform with minimum hardware requirements for running an NGS pipeline.
影响因子：
7
作者：
Giardine, B;Riemer, C;Nekrutenko, A
通讯作者：
Nekrutenko, A