title: Highly sensitive and ultrafast read mapping for RNA-seq analysis.
abstract: As sequencing technologies progress, the amount of data produced grows exponentially, shifting the bottleneck of discovery towards the data analysis phase. In particular, currently available mapping solutions for RNA-seq leave room for improvement in terms of sensitivity and performance, hindering an efficient analysis of transcriptomes by massive sequencing. Here, we present an innovative approach that combines re-engineering, optimization and parallelization. This solution results in a significant increase of mapping sensitivity over a wide range of read lengths and substantial shorter runtimes when compared with current RNA-seq mapping methods available.
authors.affiliation: HPC Service, UIS, University of Cambridge, Cambridge, UK.
authors.forename: I
authors.initials: I
authors.lastname: Medina
authors.affiliation: Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.
authors.forename: J
authors.initials: J
authors.lastname: Tárraga
authors.affiliation: Departamento de Ingeniería y Ciencia de Computadores, Universitat Jaume I, Castellón de la Plana, Spain.
authors.forename: H
authors.initials: H
authors.lastname: Martínez
authors.affiliation: Departamento de Ingeniería y Ciencia de Computadores, Universitat Jaume I, Castellón de la Plana, Spain.
authors.forename: S
authors.initials: S
authors.lastname: Barrachina
authors.affiliation: Departamento de Ingeniería y Ciencia de Computadores, Universitat Jaume I, Castellón de la Plana, Spain.
authors.forename: M I
authors.initials: MI
authors.lastname: Castillo
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: J
authors.initials: J
authors.lastname: Paschall
authors.affiliation: Instituto de Instrumentación para Imagen Molecular, Universitat Politècnica de València, Valencia, Spain.
authors.forename: J
authors.initials: J
authors.lastname: Salavert-Torres
authors.affiliation: Instituto de Instrumentación para Imagen Molecular, Universitat Politècnica de València, Valencia, Spain Grupo de Investigación Biomédica de Imagen (GIBI 2^30), La Fe Polytechnic University Hospital, Valencia, Spain.
authors.forename: I
authors.initials: I
authors.lastname: Blanquer-Espert
authors.affiliation: Instituto de Instrumentación para Imagen Molecular, Universitat Politècnica de València, Valencia, Spain.
authors.forename: V
authors.initials: V
authors.lastname: Hernández-García
authors.affiliation: Departamento de Ingeniería y Ciencia de Computadores, Universitat Jaume I, Castellón de la Plana, Spain.
authors.forename: E S
authors.initials: ES
authors.lastname: Quintana-Ortí
authors.affiliation: Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain Functional Genomics Node, (INB) at CIPF, Valencia, Spain CIBER de Enfermedades Raras (CIBERER), Valencia, Spain jdopazo@cipf.es.
authors.forename: J
authors.initials: J
authors.lastname: Dopazo
mesh_terms: D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome
keywords: Burrows-Wheeler Transform; RNA-seq; high-performance computing; mapping