José Salavert Torres

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General Purpose Graphic Processing Units (GPGPUs) constitute an inexpensive resource for computing-intensive applications that could exploit an intrinsic fine-grain parallelism. This paper presents the design and implementation in GPGPUs of an exact alignment tool for nucleotide sequences based on the Burrows-Wheeler Transform. We compare this algorithm(More)
An important effort has been invested on improving the image diagnosis process in different medical areas using information technologies. The field of medical imaging involves two main data types: medical imaging and reports. Developments based on the DICOM standard have demonstrated to be a convenient and widespread solution among the medical community.(More)
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(More)
Integrating medical data at inter-centre level implies many challenges that are being tackled from many disciplines and technologies. Medical informatics have applied an important effort on describing and standardizing Electronic Health Records, and specially standardisation has achieved an important extent on Medical Imaging. Grid technologies have been(More)
Error correction is the first step for any de novo assembly using next generation sequencing (NGS) data. This task is quite difficult and most available error correction software only supports base mismatches. In this work we propose a novel approach based on spectral graph clustering and Smith-Waterman alignment. This approach not only supports insertions(More)
The problem of sharing medical information among different centres has been tackled by many projects. Several of them target the specific problem of sharing DICOM images and structured reports (DICOM-SR), such as the TRENCADIS project. In this paper we propose sharing and organizing DICOM data and DICOM-SR metadata benefiting from the existent deployed Grid(More)
Due to the NGS data deluge, sequence mapping has become an intensive task that, depending on the experiment, may demand high amounts of computing power or memory capacity. On the one hand, GPGPU architectures have become a cost-effective solution that outperforms common processors in specific tasks. On the other hand, out-of-core implementations allow to(More)
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