Browsing by Author "Marco-Sola, Santiago"
Now showing items 1-11 of 11
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Accelerating edit-distance sequence alignment on GPU using the wavefront algorithm
(Institute of Electrical and Electronics Engineers (IEEE), 2022-06-10)
Article
Open AccessSequence alignment remains a fundamental problem with practical applications ranging from pattern recognition to computational biology. Traditional algorithms based on dynamic programming are hard to parallelize, require ... -
An FPGA accelerator of the wavefront algorithm for genomics pairwise alignment
(Institute of Electrical and Electronics Engineers (IEEE), 2021)
Conference report
Open AccessIn the last years, advances in next-generation sequencing technologies have enabled the proliferation of genomic applications that guide personalized medicine. These applications have an enormous computational cost due to ... -
AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication
(2022-01-04)
Article
Open AccessMillions of species are currently being sequenced, and their genomes are being compared. Many of them have more complex genomes than model systems and raise novel challenges for genome alignment. Widely used local alignment ... -
Efficient approximate string matching techniques for sequence alignment
(Universitat Politècnica de Catalunya, 2017-09-20)
Doctoral thesis
Open AccessOne of the outstanding milestones achieved in recent years in the field of biotechnology research has been the development of high-throughput sequencing (HTS). Due to the fact that at the moment it is technically impossible ... -
Fast gap-affine pairwise alignment using the wavefront algorithm
(2020-09-11)
Article
Open AccessMotivation Pairwise alignment of sequences is a fundamental method in modern molecular biology, implemented within multiple bioinformatics tools and libraries. Current advances in sequencing technologies press for the ... -
OpenCL-based FPGA accelerator for semi-global approximate string matching using diagonal bit-vectors
(Institute of Electrical and Electronics Engineers (IEEE), 2021)
Conference report
Open AccessAn FPGA accelerator for the computation of the semi-global Levenshtein distance between a pattern and a reference text is presented. The accelerator provides an important benefit to reduce the execution time of read-mappers ... -
RISC-V for genome data analysis: opportunities and challenges
(Institute of Electrical and Electronics Engineers (IEEE), 2023)
Conference report
Open AccessThe RISC-V ISA has gained significant momentum in High-Performance Computing (HPC) research and market due to its open-source nature, fostering collaborative research and innovation. The ever-growing RISC-V-based ... -
Sargantana: A 1 GHz+ in-order RISC-V processor with SIMD vector extensions in 22nm FD-SOI
(Institute of Electrical and Electronics Engineers (IEEE), 2022)
Conference report
Open AccessThe RISC-V open Instruction Set Architecture (ISA) has proven to be a solid alternative to licensed ISAs. In the past 5 years, a plethora of industrial and academic cores and accelerators have been developed implementing ... -
The DeepHealth Toolkit: A unified framework to boost biomedical applications
(Institute of Electrical and Electronics Engineers (IEEE), 2021)
Conference report
Open AccessGiven the overwhelming impact of machine learning on the last decade, several libraries and frameworks have been developed in recent years to simplify the design and training of neural networks, providing array-based ... -
WFA-FPGA: An efficient accelerator of the wavefront algorithm for short and long read genomics alignment
(Elsevier, 2023-12)
Article
Open AccessIn the last years, advances in genome sequencing technologies have enabled the proliferation of genomic applications that guide personalized medicine. These applications have an enormous computational cost due to the large ... -
WFA-GPU: Gap-affine pairwise read-alignment using GPUs
(2023-12)
Article
Open AccessMotivation: Advances in genomics and sequencing technologies demand faster and more scalable analysis methods that can process longer sequences with higher accuracy. However, classical pairwise alignment methods, based on ...
