title: TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing.
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.
authors.affiliation: Departamento de biodiversidad y biología evolutiva, Museo Nacional de Ciencias Naturales MNCN (CSIC), Madrid, Spain.
authors.forename: Etienne
authors.initials: E
authors.lastname: Kornobis
authors.affiliation: Instituto de Física de Cantabria, IFCA (CSIC-UC), Edificio Juan Jordá, Santander, Spain.
authors.forename: Luis
authors.initials: L
authors.lastname: Cabellos
authors.affiliation: Instituto de Física de Cantabria, IFCA (CSIC-UC), Edificio Juan Jordá, Santander, Spain.
authors.forename: Fernando
authors.initials: F
authors.lastname: Aguilar
authors.affiliation: Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
authors.forename: Cristina
authors.initials: C
authors.lastname: Frías-López
authors.affiliation: Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
authors.forename: Julio
authors.initials: J
authors.lastname: Rozas
authors.affiliation: Instituto de Física de Cantabria, IFCA (CSIC-UC), Edificio Juan Jordá, Santander, Spain.
authors.forename: Jesús
authors.initials: J
authors.lastname: Marco
authors.affiliation: Departamento de biodiversidad y biología evolutiva, Museo Nacional de Ciencias Naturales MNCN (CSIC), Madrid, Spain.
authors.forename: Rafael
authors.initials: R
authors.lastname: Zardoya
keywords: RNA-seq; annotation; de novo assembly; expression quantification; read cleaning; transcriptomics