A Collection of Papers on Genome Accelerators, from 2018 to Now.
Searching for Potential gRNA Off-Target Sites for CRISPR/Cas9 Using Automata Processing Across Different Platforms, UVA
Darwin: A Genomics Co-processor Provides up to 15000X Acceleration on Long Read Assembly, Stanford University
GenAx: A Genome Sequencing Accelerator, UofM
NONE
Darwin-WGA: A Co-processor Provides Increased Sensitivity in Whole Genome Alignments with High Speed, Stanford University
FPGA Accelerated INDEL Realignment in the Cloud, UCB
NONE
NONE
GenCache: Leveraging In-Cache Operators for Efficient Sequence Alignment, University of Utah
MEDAL: Scalable DIMM-based Near Data Processing Accelerator for DNA Seeding Algorithm, UCSB
NONE
NONE
Genesis: A Hardware Acceleration Framework for Genomic Data Analysis, SNU
SeedEx: A Genome Sequencing Accelerator for Optimal Alignments in Subminimal Space, UofM
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis, ETHZ
EXMA: A Genomics Accelerator for Exact-Matching, Indiana University Bloomington
NONE
Accelerated Seeding for Genome Sequence Alignment with Enumerated Radix Trees, UofM
Sieve: Scalable In-situ DRAM-based Accelerator Designs for Massively Parallel k-mer Matching, UVA
SquiggleFilter: An Accelerator for Portable Virus Detection, UofM
NONE
GenStore: a high-performance in-storage processing system for genome sequence analysis, ETHZ
ProSE: the architecture and design of a protein discovery engine, Duke
SeGraM: a universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping, ETHZ
BioHD: an efficient genome sequence search platform using HyperDimensional memorization, UCI
BEACON: Scalable Near-Data-Processing Accelerators for Genome Analysis near Memory Pool with the CXL Support, UCSB
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping, ETHZ
NvWa: Enhancing Sequence Alignment Accelerator Throughput via Hardware Scheduling, ICT,CAS
NONE
GenDP: A Framework of Dynamic Programming Acceleration for Genome Sequencing Analysis, UofM
Swordfish: A Framework for Evaluating Deep Neural Network-based Basecalling using Computation-In-Memory with Non-Ideal Memristors, ETHZ
DASH-CAM: Dynamic Approximate SearcH Content Addressable Memory for genome classification, Bar-Ilan University
CASA: An Energy-Efficient and High-Speed CAM-based SMEM Seeding Accelerator for Genome Alignment, THU
GMX: Instruction Set Extensions for Fast, Scalable, and Efficient Genome Sequence Alignment, Barcelona Supercomputing Center
TALCO: Tiling Genome Sequence Alignment Using Convergence of Traceback Pointers, UCSD
Harp: Leveraging Quasi-Sequential Characteristics to Accelerate Sequence-to-Graph Mapping of Long Reads, THU
QUETZAL: Vector Acceleration Framework For Modern Genome Sequence Analysis, ETHZ
TBD...