Space efficient sequence alignment for sram-based computing: X-drop on the graphcore IPU
Dedicated accelerator hardware has become essential for processing AI-based workloads,
leading to the rise of novel accelerator architectures. Furthermore, fundamental differences …
leading to the rise of novel accelerator architectures. Furthermore, fundamental differences …
Harnessing the power of idle GPUs for acceleration of biological sequence alignment
F Ino, Y Kotani, Y Munekawa… - Parallel Processing …, 2009 - World Scientific
This paper presents a parallel system capable of accelerating biological sequence
alignment on the graphics processing unit (GPU) grid. The GPU grid in this paper is a …
alignment on the graphics processing unit (GPU) grid. The GPU grid in this paper is a …
GSWABE: faster GPU‐accelerated sequence alignment with optimal alignment retrieval for short DNA sequences
In this paper, we present GSWABE, a graphics processing unit (GPU)‐accelerated pairwise
sequence alignment algorithm for a collection of short DNA sequences. This algorithm …
sequence alignment algorithm for a collection of short DNA sequences. This algorithm …
GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data
Background Due the computational complexity of sequence alignment algorithms, various
accelerated solutions have been proposed to speedup this analysis. NVBIO is the only …
accelerated solutions have been proposed to speedup this analysis. NVBIO is the only …
Adept: a domain independent sequence alignment strategy for gpu architectures
Background Bioinformatic workflows frequently make use of automated genome assembly
and protein clustering tools. At the core of most of these tools, a significant portion of …
and protein clustering tools. At the core of most of these tools, a significant portion of …
A High-Performance Genomic Accelerator for Accurate Sequence-to-Graph Alignment Using Dynamic Programming Algorithm
The rapid mutation of viruses, such as SARS-CoV-2, highlights the urgent need for fast and
precise genomic sequencing. The traditional sequencing technique maps the DNA …
precise genomic sequencing. The traditional sequencing technique maps the DNA …
pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment
S Warris, NRN Timal, M Kempenaar, AM Poortinga… - PLoS …, 2018 - journals.plos.org
Background Our previously published CUDA-only application PaSWAS for Smith-Waterman
(SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform …
(SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform …
Rapidx: High-performance reram processing in-memory accelerator for sequence alignment
Genome sequence alignment is the core of many biological applications. The advancement
of sequencing technologies produces a tremendous amount of data, making sequence …
of sequencing technologies produces a tremendous amount of data, making sequence …
On the genome sequence alignment fpga acceleration via ksw2z
Pairwise sequence alignment is a fundamental step for many genomics and molecular
biology applications. Given the quadratic time complexity of alignment algorithms, the …
biology applications. Given the quadratic time complexity of alignment algorithms, the …
Faster sequence alignment through GPU-accelerated restriction of the seed-and-extend search space
Motivation In computing pairwise alignments of biological sequences, software
implementations employ a variety of heuristics that decrease the computational effort …
implementations employ a variety of heuristics that decrease the computational effort …