Kronos: a workflow assembler for genome analytics and informatics
Creators: name: M Jafar Taghiyar
name: Rosner, Jamie
name: Diljot Grewal
name: Grande, Bruno
name: Radhouane Aniba
name: Jasleen Grewal
name: Boutros, Paul C
name: Morin, Ryan D
name: Bashashati, Ali
name: Shah, Sohrab P
Publisher: name: F1000Research
Year: 2016

description: <i>Background</i><br>The field of next generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. However, practical and robust implementation of complex analytical workflows still requires significant programming investment and expertise. For example, analysis of cancer genomes may invoke sequence alignment followed by mutation, copy number, and rearrangement detection, followed by annotation of predicted functional effects of these alterations.  In both research and clinical settings it is vital to encode specific analytical protocols for transparency of derivative results and clinical audits.<br><i>Results</i><br>We present Kronos, a software platform for automating the development and execution of reproducible, auditable and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by transforming a text configuration file into an executable Python script. Given a set of existing components (analysis modules), a new workflow can be created in three simple steps:<br><i>Step 1.</i> Create a configuration file template by running <i>kronos</i> <i>make_config</i> command.<br><i>Step 2.</i> In the template, specify the order by which the  components in the workflow should be run.<br><i>Step 3.</i> Create the workflow by running <i>kronos</i> <i>init</i> command with  the template as input.<br> The result is an executable Python script that uses the built-in run manager of Kronos. The run manager provides scalability by enabling users to run the workflow on a single machine or a cluster of computing nodes. Moreover, each component in the workflow can individually be run either locally, or on a cluster. Workflows created by Kronos are highly modular and configurable through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, promoting and facilitating reproducible research and comparative analyses. Kronos also has a framework for making components. Each component is an analysis module wrapped according to the framework. A component template can be made using <i>kronos</i> <i>make_component </i>command.  Developers can use the framework to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with Docker and Amazon AWS machine images. It is free, open source and available through Python Package Index.<br><i>Conclusion</i><br>This work provides a framework towards rapid integration of new (and optimal) genomic analysis advances in high-throughput studies. The flexibility, customization, and modularity of the resulting pipelines make it an attractive system to use in any high-throughput genomics analysis endeavour. We expect Kronos will be a small but foundational step towards standardization and distribution of NGS workflows in both clinical and research applications.<br>