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2015-05-24

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cc-by-nc (c) Kornobis, Etienne et al., 2015
Please use this identifier to cite or link to this item: https://hdl.handle.net/2445/96313

TRUFA: A user-friendly web server for de novo RNA-seq analysis using cluster computing.

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http://dx.doi.org/10.4137/EBO.S23873

Abstract

Application of next-generation sequencing (NGS) methods for transcriptome analysis (RNA-seq) has become increasingly accessible in recent years and are of great interest to many biological disciplines including, eg, evolutionary biology, ecology, biomedicine, and computational biology. Although virtually any research group can now obtain RNA-seq data, only a few have the bioinformatics knowledge and computation facilities required for transcriptome analysis. Here, we present TRUFA (TRanscriptome User-Friendly Analysis), an open informatics platform offering a web-based interface that generates the outputs commonly used in de novo RNA-seq analysis and comparative transcriptomics. TRUFA provides a comprehensive service that allows performing dynamically raw read cleaning, transcript assembly, annotation, and expression quantification. Due to the computationally intensive nature of such analyses, TRUFA is highly parallelized and benefits from accessing high-performance computing resources. The complete TRUFA pipeline was validated using four previously published transcriptomic data sets. TRUFA's results for the example datasets showed globally similar results when comparing with the original studies, and performed particularly better when analyzing the green tea dataset. The platform permits analyzing RNA-seq data in a fast, robust, and user-friendly manner. Accounts on TRUFA are provided freely upon request at https://trufa.ifca.es.

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Transcripció genètica, Bioinformàtica, RNA

Subject (English)

Genetic transcription, Bioinformatics, RNA

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Articles publicats en revistes (Genètica, Microbiologia i Estadística)

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KORNOBIS, Etienne, et al. TRUFA: A user-friendly web server for de novo RNA-seq analysis using cluster computing. Evolutionary Bioinformatics. 2015. Vol. 11, num. 97-104. ISSN 1176-9343. [consulted: 8 of August of 2026]. Available at: https://hdl.handle.net/2445/96313

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