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Abstract
BackgroundThe emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) is transforming biological research. The dramatic increase in the volume of data, the variety and continuous change of data processing tools, algorithms and databases make analysis the main bottleneck for scientific discovery. The processing of high throughput datasets typically involves many different computational programs, each of which performs a specific step in a pipeline. Given the wide range of applications and organizational infrastructures, there is a great need for highly parallel, flexible, portable, and reproducible data processing frameworks.Several platforms currently exist for the design and execution of complex pipelines. Unfortunately, current platforms lack the necessary combination of parallelism, portability, flexibility and/or reproducibility that are required by the current research environment. To address these shortcomings, workflow frameworks that provide a platform to develop and share portable pipelines have recently arisen. We complement these new platforms by providing a graphical user interface to create, maintain, and execute complex pipelines. Such a platform will simplify robust and reproducible workflow creation for non-technical users as well as provide a robust platform to maintain pipelines for large organizations.ResultsTo simplify development, maintenance, and execution of complex pipelines we created DolphinNext. DolphinNext facilitates building and deployment of complex pipelines using a modular approach implemented in a graphical interface that relies on the powerful Nextflow workflow framework by providing 1. A drag and drop user interface that visualizes pipelines and allows users to create pipelines without familiarity in underlying programming languages. 2. Modules to execute and monitor pipelines in distributed computing environments such as high-performance clusters and/or cloud 3. Reproducible pipelines with version tracking and stand-alone versions that can be run independently. 4. Modular process design with process revisioning support to increase reusability and pipeline development efficiency. 5. Pipeline sharing with GitHub and automated testing 6. Extensive reports with R-markdown and shiny support for interactive data visualization and analysis.ConclusionDolphinNext is a flexible, intuitive, web-based data processing and analysis platform that enables creating, deploying, sharing, and executing complex Nextflow pipelines with extensive revisioning and interactive reporting to enhance reproducible results.
Highlights
The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) is transforming biological research
Microarray analysis became widely accessible only with the availability of several public and commercial platforms, such as GenePattern [3] and Affymetrix [4], that provided a user interface to simplify the application of a diverse set of methods to process and analyze raw microarray data
Sequence analysis requires an iterative approach that consists of two main tasks: data processing and data analysis [38] (Fig. 6)
Summary
The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) is transforming biological research. Current platforms lack the necessary combination of parallelism, portability, flexibility and/or reproducibility that are required by the current research environment. To address these shortcomings, workflow frameworks that provide a platform to develop and share portable pipelines have recently arisen. Workflow frameworks that provide a platform to develop and share portable pipelines have recently arisen We complement these new platforms by providing a graphical user interface to create, maintain, and execute complex pipelines. Microarray analysis became widely accessible only with the availability of several public and commercial platforms, such as GenePattern [3] and Affymetrix [4], that provided a user interface to simplify the application of a diverse set of methods to process and analyze raw microarray data
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