Browsing by Author "Castells Rufas, David"
Now showing items 1-5 of 5
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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 ... -
Ethernet emulation over PCIe for RISC-V software development vehicles
(Institute of Electrical and Electronics Engineers (IEEE), 2023)
Conference report
Open AccessThis paper describes two different approaches to emulate an Ethernet communication link between a host computer and a RISC-V multiprocessor system running on a FPGA accelerator by using PCIe as the real communication link. ... -
FPGA Acceleration of Pre-Alignment Filters for Short Read Mapping With HLS
(Institute of Electrical and Electronics Engineers (IEEE), 2022-02)
Article
Open AccessPre-alignment filters are useful for reducing the computational requirements of genomic sequence mappers. Most of them are based on estimating or computing the edit distance between sequences and their candidate locations ... -
GPU acceleration of Levenshtein distance computation between long strings
(Elsevier, 2023)
Article
Open AccessComputing edit distance for very long strings has been hampered by quadratic time complexity with respect to string length. The WFA algorithm reduces the time complexity to a quadratic factor with respect to the edit ... -
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 ...
