Source code for the software implementations of the GenASM algorithms proposed in our MICRO 2020 paper: Senol Cali et. al., "GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis" at https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analys…
☆32Dec 19, 2022Updated 3 years ago
Alternatives and similar repositories for GenASM
Users that are interested in GenASM are comparing it to the libraries listed below
Sorting:
- Source code of the processing-in-memory simulator used in the GRIM-Filter paper published at BMC Genomics in 2018: "GRIM-Filter: Fast See…☆11Feb 5, 2018Updated 8 years ago
- AIM, A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems, Bioinformatics, btad155, https://doi.or…☆22Apr 12, 2023Updated 2 years ago
- AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shar…☆28May 23, 2024Updated last year
- SneakySnake is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU arch…☆54Mar 31, 2023Updated 2 years ago
- GateKeeper: Fast Alignment Filter for DNA Short Read Mapping☆21Mar 5, 2019Updated 6 years ago
- micro-read Fast Alignment Search Tool☆19Jul 19, 2019Updated 6 years ago
- Source code for the Shifted Hamming Distance (SHD) filtering mechanism for sequence alignment. Described in the Bioinformatics journal pa…☆36Mar 29, 2020Updated 5 years ago
- Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a sing…☆28May 10, 2020Updated 5 years ago
- PIM-ML is a benchmark for training machine learning algorithms on the UPMEM architecture, which is the first publicly-available real-worl…☆25Jan 7, 2025Updated last year
- Cache and main memory hog programs. These are programs with specific access patterns to evict the already existing cache blocks of variou…☆21Nov 2, 2016Updated 9 years ago
- A survey of manufacturer-provided DRAM operating parameters and timings as specified by DRAM chip datasheets from between 1970 and 2021. …☆11May 4, 2022Updated 3 years ago
- Source code & scripts for experimental characterization and demonstration of 1) simultaneous many-row activation, 2) up to nine-input maj…☆11May 17, 2024Updated last year
- BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy…☆45May 10, 2023Updated 2 years ago
- Co-processor for whole genome alignment☆13Jun 6, 2020Updated 5 years ago
- TransPimLib is a library for transcendental (and other hard-to-calculate) functions in general-purpose PIM systems, TransPimLib provides …☆15Apr 21, 2023Updated 2 years ago
- PyGim is the first runtime framework to efficiently execute Graph Neural Networks (GNNs) on real Processing-in-Memory systems. It provide…☆33Apr 23, 2025Updated 10 months ago
- Source code for the architectural and circuit-level simulators used for modeling the CROW (Copy-ROW DRAM) mechanism proposed in our ISCA …☆15Aug 2, 2019Updated 6 years ago
- GenStore is the first in-storage processing system designed for genome sequence analysis that greatly reduces both data movement and comp…☆15Apr 6, 2022Updated 3 years ago
- ☆15Dec 15, 2022Updated 3 years ago
- Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metag…☆17Sep 4, 2024Updated last year
- This simulator models multi core systems with primary focus on the memory hierarchy. It models a trace-based out-of-order core frontend a…☆12Feb 12, 2016Updated 10 years ago
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆38Jun 23, 2023Updated 2 years ago
- NATSA is the first near-data-processing accelerator for time series analysis based on the Matrix Profile (SCRIMP) algorithm. NATSA exploi…☆16Jun 14, 2023Updated 2 years ago
- A comprehensive content-addressable accelerator simulation framework.