Dataset Information

Kronos: a workflow assembler for genome analytics and informatics.

ABSTRACT: Background: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. Practical and robust implementation of complex analytical workflows (where such tools are structured into "best practices" for automated analysis of next-generation sequencing datasets) still requires significant programming investment and expertise. Results:We present Kronos, a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by compiling a text configuration file into executable Python applications. Making analysis modules would still require programming. The framework of each workflow includes a run manager to execute the encoded workflows locally (or on a cluster or cloud), parallelize tasks, and log all runtime events. The resulting workflows are highly modular and configurable by construction, facilitating flexible and extensible meta-applications that can be modified easily through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, a step toward reproducible research and comparative analyses. We introduce a framework for building Kronos components that function as shareable, modular nodes in Kronos workflows. Conclusions:The Kronos platform provides a standard framework for developers to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with both Docker and Amazon Web Services Machine Images. It is free, open source, and available through the Python Package Index and at https://github.com/jtaghiyar/kronos.

SUBMITTER: Taghiyar MJ

PROVIDER: S-EPMC5569921 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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Kronos: a workflow assembler for genome analytics and informatics.

Taghiyar M Jafar MJ Rosner Jamie J Grewal Diljot D Grande Bruno M BM Aniba Radhouane R Grewal Jasleen J Boutros Paul C PC Morin Ryan D RD Bashashati Ali A Shah Sohrab P SP

GigaScience 20170701 7

<h4>Background</h4>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. Practical and robust implementation of complex analytical workflows (where such tools are structured into "best practices" for automated analysis of next-generation sequencing datasets) still requires significant programming investment and expertise.<h4>Results</h4>We present Kronos, a software pla ...[more]

PMID: 28655203

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Project description:IntroductionWe define a designated data analytics workflow for the evaluation of stability experiments, which takes all data situations into account. This complements the evaluation described by the CLSI EP25 [1] guideline by including a targeted exception handling algorithm and thus allows one to automatically evaluate stability data based on linear regression analysis.DescriptionThe evaluation of stability experiments based on regression analysis requires the calculation of the confidence interval of the regression line. The stability time is estimated at the intersection of the confidence interval with the acceptance criterion. This approach results in solving a quadratic equation, with factors that depend on the estimated intercept, slope, the measurement variability and the chosen timepoints. When defining an automated data analytics workflow for this problem, the different cases for the solutions of the quadratic equation must be considered. For some data situations there might be no solution at all, other data situations result in a negative and a positive solution and finally there might be even two positive solutions. All these cases have to be considered for the choice of the right solution to become the estimated stability time. The CLSI EP25 [1] guideline on stability evaluation of in vitro diagnostic reagents addresses this problem only superficially and might even lead to incorrect results for some specific data scenarios.ResultsWe evaluate all possible data scenarios and provide examples for each. Based on the gained theoretical insights, we define a designated data analytics workflow and visualize it with a flowchart. By following this flowchart one can implement an automated analysis workflow, targeting all data scenarios with the appropriate exception handling.DiscussionWe deduce that the description for obtaining stability times according to CLSI EP25 is not fully adequate, as it addresses only best-case scenarios. However, for automated data analytics workflows all possible data situations have to be considered. With the here presented workflow one can program automated data analytics pipelines, which ensure that the right stability time is obtained, in case it exists. In addition all exceptions, where no stability times are present, are addressed in the right way and it provides hints as to the failure reason.

Dataset Information

Kronos: a workflow assembler for genome analytics and informatics.

Publications

Kronos: a workflow assembler for genome analytics and informatics.

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