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- W4289244058 abstract "Sliding window sums are widely used in bioinformatics applications, including sequence assembly, k-mer generation, hashing and compression. New vector algorithms which utilize the advanced vector extension (AVX) instructions available on modern processors, or the parallel compute units on GPUs and FPGAs, would provide a significant performance boost for the bioinformatics applications. We develop a generic vectorized sliding sum algorithm with speedup for window size w and number of processors P is O(P/w) for a generic sliding sum. For a sum with commutative operator the speedup is improved to O(P/log(w)). When applied to the genomic application of minimizer based k-mer table generation using AVX instructions, we obtain a speedup of over 5X." @default.
- W4289244058 created "2022-08-01" @default.
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- W4289244058 date "2018-11-25" @default.
- W4289244058 modified "2023-10-14" @default.
- W4289244058 title "Parallel approach to sliding window sums" @default.
- W4289244058 doi "https://doi.org/10.48550/arxiv.1811.10074" @default.
- W4289244058 hasPublicationYear "2018" @default.
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