Efficient architecture-aware acceleration of BWA-MEM for multicore systems

M Vasimuddin, S Misra, H Li… - 2019 IEEE international …, 2019‏ - ieeexplore.ieee.org
Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data
at ever faster rates and at very low cost. For example, the Illumina NovaSeq 6000 sequencer …

Domain adaptive faster r-cnn for object detection in the wild

Y Chen, W Li, C Sakaridis, D Dai… - Proceedings of the …, 2018‏ - openaccess.thecvf.com
Object detection typically assumes that training and test data are drawn from an identical
distribution, which, however, does not always hold in practice. Such a distribution mismatch …

BWA-MEME: BWA-MEM emulated with a machine learning approach

Y Jung, D Han - Bioinformatics, 2022‏ - academic.oup.com
Motivation The growing use of next-generation sequencing and enlarged sequencing
throughput require efficient short-read alignment, where seeding is one of the major …

Hardware acceleration of BWA-MEM genomic short read map** for longer read lengths

EJ Houtgast, VM Sima, K Bertels, Z Al-Ars - Computational biology and …, 2018‏ - Elsevier
We present our work on hardware accelerated genomics pipelines, using either FPGAs or
GPUs to accelerate execution of BWA-MEM, a widely-used algorithm for genomic short read …

Natural variation in Glume Coverage 1 causes naked grains in sorghum

P ** in genome sequencing: A race between fpga and gpu
L Guo, J Lau, Z Ruan, P Wei… - 2019 IEEE 27th Annual …, 2019‏ - ieeexplore.ieee.org
In genome sequencing, it is a crucial but time-consuming task to detect potential overlaps
between any pair of the input reads, especially those that are ultra-long. The state-of-the-art …

Medal: Scalable dimm based near data processing accelerator for dna seeding algorithm

W Huangfu, X Li, S Li, X Hu, P Gu, Y **e - … of the 52nd Annual IEEE/ACM …, 2019‏ - dl.acm.org
Computational genomics has proven its great potential to support precise and customized
health care. However, with the wide adoption of the Next Generation Sequencing (NGS) …

When Spark Meets {FPGAs}: A Case Study for {Next-Generation}{DNA} Sequencing Acceleration

YT Chen, J Cong, Z Fang, J Lei, P Wei - 8th USENIX Workshop on Hot …, 2016‏ - usenix.org
FPGA-enabled datacenters have shown great potential for providing performance and
energy efficiency improvement. In this paper we aim to answer one key question: how can …

Beacon: Scalable near-data-processing accelerators for genome analysis near memory pool with the cxl support

W Huangfu, KT Malladi, A Chang… - 2022 55th IEEE/ACM …, 2022‏ - ieeexplore.ieee.org
Genome analysis benefits precise medical care, wildlife conservation, pandemic treatment
(eg, COVID-19), and so on. Unfortunately, in genome analysis, the speed of data processing …

BioSEAL: In-memory biological sequence alignment accelerator for large-scale genomic data

R Kaplan, L Yavits, R Ginosasr - … of the 13th ACM International Systems …, 2020‏ - dl.acm.org
Genome sequences contain hundreds of millions of DNA base pairs. Finding the degree of
similarity between two genomes requires executing a compute-intensive dynamic …