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. We may earn a commission when you buy through links labeled 'Ad' on this page.
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
- ApHMM-GPU is the first GPU implementation of the Baum-Welch algorithm for profile Hidden Markov Models (pHMMs). It includes many of the s…☆11Jul 21, 2022Updated 4 years ago
- SneakySnake is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU arch…☆57Mar 31, 2023Updated 3 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 2 years ago
- AIM, A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems, Bioinformatics, btad155, https://doi.or…☆24Apr 12, 2023Updated 3 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- GateKeeper: Fast Alignment Filter for DNA Short Read Mapping☆23Mar 5, 2019Updated 7 years ago
- micro-read Fast Alignment Search Tool☆20Jul 19, 2019Updated 7 years ago
- An FPGA-accelerated version of minimap2☆11May 30, 2023Updated 3 years ago
- Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metag…☆19Sep 4, 2024Updated 2 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 4 years ago
- HLS-based framework to accelerate the implementation of 2-D DP kernels on FPGA☆15Mar 26, 2026Updated 7 months 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 6 years ago
- A benchmark suite to study the performance characteristics of genomics applications☆32Oct 21, 2024Updated 2 years ago
- Circuit-level model for the Capacity-Latency Reconfigurable DRAM (CLR-DRAM) architecture. This repository contains the SPICE models of th…☆16Sep 24, 2020Updated 6 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Darwin: A co-processor for long read alignment☆16Apr 5, 2019Updated 7 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 4 years ago
- Source code & scripts for experimental characterization and demonstration of 1) simultaneous many-row activation, 2) up to nine-input maj…☆18May 17, 2024Updated 2 years ago
- BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy…☆47May 10, 2023Updated 3 years ago
- A tracing tool to analyze the I/O behavior of a program.☆12Sep 25, 2019Updated 7 years ago
- ☆14Dec 15, 2022Updated 3 years ago
- Source code for the architectural and circuit-level simulators used for modeling the CROW (Copy-ROW DRAM) mechanism proposed in our ISCA …☆18Aug 2, 2019Updated 7 years ago
- A new DRAM substrate that mitigates the excessive energy consumption from both (i) transmitting unused data on the memory channel and (i…☆14Aug 23, 2024Updated 2 years ago
- PIM-ML is a benchmark for training machine learning algorithms on the UPMEM architecture, which is the first publicly-available real-worl…☆30Jan 7, 2025Updated last year
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Co-processor for whole genome alignment☆13Jun 6, 2020Updated 6 years ago
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆38Jun 23, 2023Updated 3 years ago
- 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
- HWASim is a simulator for heterogeneous systems with CPUs and Hardware Accelerators (HWAs). It is released with the DASH memory scheduler…☆19Jan 11, 2016Updated 10 years ago
- TransPimLib is a library for transcendental (and other hard-to-calculate) functions in general-purpose PIM systems, TransPimLib provides …☆15Apr 21, 2023Updated 3 years ago
- FastRemap, a C++ tool for quickly remapping reads between genome assemblies based on the commonly used CrossMap tool. Link to paper: http…☆26Aug 24, 2022Updated 4 years ago
- pLUTo is a DRAM-based Processing-using-Memory architecture that leverages the high density of DRAM to enable the massively parallel stori…☆20Jan 12, 2023Updated 3 years ago
- PyGim is the first runtime framework to efficiently execute Graph Neural Networks (GNNs) on real Processing-in-Memory systems. It provide…☆36Apr 23, 2025Updated last year
- NATSA is the first near-data-processing accelerator for time series analysis based on the Matrix Profile (SCRIMP) algorithm. NATSA exploi…☆17Jun 14, 2023Updated 3 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Source code & scripts for experimental characterization and demonstration of performing NOT and up to 16-input AND, NAND, OR, and NOR ope…☆15Apr 9, 2024Updated 2 years ago
- Chai☆51Nov 14, 2025Updated 11 months ago
- FASTR, an efficient file format designed for lossless storage of sequencing data as numerical formats. Read more: https://www.biorxiv.org…☆12Oct 5, 2026Updated 3 weeks ago
- DAMOV is a benchmark suite and a methodical framework targeting the study of data movement bottlenecks in modern applications. It is inte…☆97Jul 27, 2023Updated 3 years ago
- ☆23Feb 18, 2025Updated last year
- Source code for the architectural simulator used for modeling the PUD system proposed in our HPCA 2024 paper `MIMDRAM: An End-to-End Proc…☆36Sep 12, 2025Updated last year
- A tool for detecting and analyzing runtime phases☆12Dec 30, 2015Updated 10 years ago