Hardware acceleration of genomics data analysis: challenges and opportunities
The significant decline in the cost of genome sequencing has dramatically changed the
typical bioinformatics pipeline for analysing sequencing data. Where traditionally, the …
typical bioinformatics pipeline for analysing sequencing data. Where traditionally, the …
SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs
Abstract Motivation We introduce SneakySnake, a highly parallel and highly accurate pre-
alignment filter that remarkably reduces the need for computationally costly sequence …
alignment filter that remarkably reduces the need for computationally costly sequence …
Shouji: a fast and efficient pre-alignment filter for sequence alignment
Motivation The ability to generate massive amounts of sequencing data continues to
overwhelm the processing capability of existing algorithms and compute infrastructures. In …
overwhelm the processing capability of existing algorithms and compute infrastructures. In …
Banking with precision: transfusion medicine as a potential universal application in clinical genomics
C Montemayor, PAR Brunker… - Current opinion in …, 2019 - journals.lww.com
Banking with precision: transfusion medicine as a potential... : Current Opinion in
Hematology Banking with precision: transfusion medicine as a potential universal …
Hematology Banking with precision: transfusion medicine as a potential universal …
New evaluation methods of read mapping by 17 aligners on simulated and empirical NGS data: an updated comparison of DNA-and RNA-Seq data from Illumina and …
L Donato, C Scimone, C Rinaldi, R D'Angelo… - Neural Computing and …, 2021 - Springer
Abstract During the last (15) years, improved omics sequencing technologies have
expanded the scale and resolution of various biological applications, generating high …
expanded the scale and resolution of various biological applications, generating high …
Fpga acceleration of sequence alignment: A survey
Genomics is changing our understanding of humans, evolution, diseases, and medicines to
name but a few. As sequencing technology is developed collecting DNA sequences takes …
name but a few. As sequencing technology is developed collecting DNA sequences takes …
Understanding the bioinformatics challenges of integrating genomics into healthcare
Genomic data are paving the way toward personalized healthcare. By unveiling genetic
disease-contributing factors, genomic data can aid in the detection, diagnosis, and treatment …
disease-contributing factors, genomic data can aid in the detection, diagnosis, and treatment …
Sparkflow: Towards high-performance data analytics for spark-based genome analysis
The recent advances in DNA sequencing technology triggered next-generation sequencing
(NGS) research in full scale. Big Data (BD) is becoming the main driver in analyzing these …
(NGS) research in full scale. Big Data (BD) is becoming the main driver in analyzing these …
Salient: Ultra-fast fpga-based short read alignment
B Khaleghi, T Zhang, C Martino… - … Conference on Field …, 2022 - ieeexplore.ieee.org
State-of-the-art high-throughput DNA sequencers output terabytes of short reads that
typically need to be aligned to a reference genome in order to perform downstream …
typically need to be aligned to a reference genome in order to perform downstream …
Motif identification using CNN-based pairwise subsequence alignment score prediction
A common problem in bioinformatics is related to identifying gene regulatory regions marked
by relatively high frequencies of motifs, or deoxyribonucleic acid sequences that often code …
by relatively high frequencies of motifs, or deoxyribonucleic acid sequences that often code …