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Gigascience. 2014 Oct 13;3:19. doi: 10.1186/2047-217X-3-19. eCollection 2014.

iReport: a generalised Galaxy solution for integrated experimental reporting.

Author information

1
Department of Bioinformatics, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands ; Department of Urology, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands.
2
Department of Bioinformatics, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands.
3
Department of Urology, Erasmus Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands.

Abstract

BACKGROUND:

Galaxy offers a number of visualisation options with components, such as Trackster, Circster and Galaxy Charts, but currently lacks the ability to easily combine outputs from different tools into a single view or report. A number of tools produce HTML reports as output in order to combine the various output files from a single tool; however, this requires programming and knowledge of HTML, and the reports must be custom-made for each new tool.

FINDINGS:

We have developed a generic and flexible reporting tool for Galaxy, iReport, that allows users to create interactive HTML reports directly from the Galaxy UI, with the ability to combine an arbitrary number of outputs from any number of different tools. Content can be organised into different tabs, and interactivity can be added to components. To demonstrate the capability of iReport we provide two publically available examples, the first is an iReport explaining about iReports, created for, and using content from the recent Galaxy Community Conference 2014. The second is a genetic report based on a trio analysis to determine candidate pathogenic variants which uses our previously developed Galaxy toolset for whole-genome NGS analysis, CGtag. These reports may be adapted for outputs from any sequencing platform and any results, such as omics data, non-high throughput results and clinical variables.

CONCLUSIONS:

iReport provides a secure, collaborative, and flexible web-based reporting system that is compatible with Galaxy (and non-Galaxy) generated content. We demonstrate its value with a real-life example of reporting genetic trio-analysis.

KEYWORDS:

Galaxy; Generic reporting application; Genetic variation; Next generation sequencing; Pathogenic gene selection

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