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Updated: Apr 25, 2026

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
Published on: March 15, 2019
Acceleration of short and long DNA read mapping without loss of accuracy using suffix array
Joaquín Tárraga1, Vicente Arnau2, Héctor Martínez2
1Department of Computational Genomics, Centro de Investigación Príncipe Felipe (CIPF), Functional Genomics Node, (INB) at CIPF 46012, Departamento de Informática, Universidad de Valencia, 46100 Valencia, Departamento de Ingeniería y Ciencia de Computadores, Universitat Jaume I, 12071 Castellón de la Plana, Instituto de Investigación en Informática de Albacete, Universidad de Castilla-La Mancha, Campus Universitario, 02071 Albacete, Universitat Politècnica de València, Instituto de Instrumentación para Imagen Molecular, 46022 Valencia, Grupo de Investigación Biomédica de Imagen (GIBI 2^30), La Fe Polytechnic University Hospital, 46022 Valencia and Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, Spain Department of Computational Genomics, Centro de Investigación Príncipe Felipe (CIPF), Functional Genomics Node, (INB) at CIPF 46012, Departamento de Informática, Universidad de Valencia, 46100 Valencia, Departamento de Ingeniería y Ciencia de Computadores, Universitat Jaume I, 12071 Castellón de la Plana, Instituto de Investigación en Informática de Albacete, Universidad de Castilla-La Mancha, Campus Universitario, 02071 Albacete, Universitat Politècnica de València, Instituto de Instrumentación para Imagen Molecular, 46022 Valencia, Grupo de Investigación Biomédica de Imagen (GIBI 2^30), La Fe Polytechnic University Hospital, 46022 Valencia and Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.
Unlabelled:
HPG Aligner applies suffix arrays for DNA read mapping. This implementation produces a highly sensitive and extremely fast mapping of DNA reads that scales up almost linearly with read length. The approach presented here is faster (over 20× for long reads) and more sensitive (over 98% in a wide range of read lengths) than the current state-of-the-art mappers. HPG Aligner is not only an optimal alternative for current sequencers but also the only solution available to cope with longer reads and growing throughputs produced by forthcoming sequencing technologies.
Availability And Implementation:
https://github.com/opencb/hpg-aligner.
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