[HTML][HTML] From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures
We now need more than ever to make genome analysis more intelligent. We need to read,
analyze, and interpret our genomes not only quickly, but also accurately and efficiently …
analyze, and interpret our genomes not only quickly, but also accurately and efficiently …
GenStore: A high-performance in-storage processing system for genome sequence analysis
Read mapping is a fundamental step in many genomics applications. It is used to identify
potential matches and differences between fragments (called reads) of a sequenced …
potential matches and differences between fragments (called reads) of a sequenced …
SeGraM: A universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments
(ie, reads) collected from an individual to a known linear reference genome sequence (ie …
(ie, reads) collected from an individual to a known linear reference genome sequence (ie …
A framework for high-throughput sequence alignment using real processing-in-memory systems
Motivation Sequence alignment is a memory bound computation whose performance in
modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory …
modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory …
GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis
Read mapping is a fundamental, yet computationally-expensive step in many genomics
applications. It is used to identify potential matches and differences between fragments …
applications. It is used to identify potential matches and differences between fragments …
Gmx: Instruction set extensions for fast, scalable, and efficient genome sequence alignment
Sequence alignment remains a fundamental problem in computer science with practical
applications ranging from pattern matching to computational biology. The ever-increasing …
applications ranging from pattern matching to computational biology. The ever-increasing …
WFA-FPGA: An efficient accelerator of the wavefront algorithm for short and long read genomics alignment
In the last years, advances in genome sequencing technologies have enabled the
proliferation of genomic applications that guide personalized medicine. These applications …
proliferation of genomic applications that guide personalized medicine. These applications …
Machine learning for agile fpga design
Field-programmable gate arrays (FPGAs) have become popular means of hardware
acceleration since they offer massive parallelism, flexible configurability, and potentially …
acceleration since they offer massive parallelism, flexible configurability, and potentially …
Genpip: In-memory acceleration of genome analysis via tight integration of basecalling and read mapping
Nanopore sequencing is a widely-used high-throughput genome sequencing technology
that can sequence long fragments of a genome into raw electrical signals at low cost …
that can sequence long fragments of a genome into raw electrical signals at low cost …
Accelerating edit-distance sequence alignment on GPU using the wavefront algorithm
Sequence alignment remains a fundamental problem with practical applications ranging
from pattern recognition to computational biology. Traditional algorithms based on dynamic …
from pattern recognition to computational biology. Traditional algorithms based on dynamic …