Source code for the software implementation of SeGraM proposed in our ISCA 2022 paper: Senol Cali et. al., "SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping" at https://people.inf.ethz.ch/omutlu/pub/SeGraM_genomic-sequence-mapping-universal-accelerator_isca22.pdf
☆13Nov 3, 2022Updated 4 years ago
Alternatives and similar repositories for SeGraM
Users that are interested in SeGraM are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- 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
- SuperSampler, an efficient scaled size sketching and sketch comparison tool☆11Nov 13, 2023Updated 2 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
- Source code for the software implementations of the GenASM algorithms proposed in our MICRO 2020 paper: Senol Cali et. al., "GenASM: A Hi…☆32Dec 19, 2022Updated 3 years ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- 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
- HLS-based framework to accelerate the implementation of 2-D DP kernels on FPGA☆15Mar 26, 2026Updated 7 months 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
- 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
- ☆29Sep 28, 2024Updated 2 years ago
- Benchmark suite containing cache filtered traces for use with Ramulator. These include some of the workloads used in our SIGMETRICS 2019 …☆24Oct 9, 2020Updated 6 years ago
- Shouji is fast and accurate pre-alignment filter for banded sequence alignment calculation. Described in the Bioinformatics journal paper…☆19Jun 3, 2019Updated 7 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
- A collection of Phylogenetics tools for creating and manipulating networks and trees.☆10Oct 12, 2017Updated 9 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- CLfinder-OrthNet, a pipeline to encode orthologs from multiple genomes and their evolutionary history into networks (OrthNets) based on c…☆10Jun 9, 2022Updated 4 years ago
- paired end distance, split reads matching, read depth are used to detect and precisely locate structure variations☆11Apr 9, 2014Updated 12 years ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆24Jan 29, 2023Updated 3 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
- A transposition caller.☆12Oct 5, 2023Updated 3 years ago
- Code to create a PRG from a Multiple Sequence Alignment file☆26Sep 10, 2025Updated last year
- Co-processor for whole genome alignment☆13Jun 6, 2020Updated 6 years ago
- Metasys is the first open-source FPGA-based infrastructure with a prototype in a RISC-V core, to enable the rapid implementation and eval…☆16Jan 20, 2023Updated 3 years ago
- SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results.☆17Dec 5, 2023Updated 2 years ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Source code for the Base-Delta-Immediate Compression Algorithm (described in the PACT 2012 paper by Pekhimenko et al. at http://users.ece…☆28Mar 1, 2015Updated 11 years ago
- CoMeT is a new low-cost RowHammer mitigation that uses Count-Min Sketch-based aggressor row tracking, as described in our HPCA'24 paper h…☆12Jan 23, 2026Updated 9 months ago
- Detailed read disturbance (RowHammer and RowPress) characterization of six real HBM2 DRAM chips yielding 23 new observations and 8 new ta…☆12May 3, 2024Updated 2 years ago
- A DDR3 Controller that uses the Xilinx MIG-7 PHY to interface with DDR3 devices.☆12Aug 22, 2021Updated 5 years ago
- A Julia package for handle genome graph in the GFA format.☆11Sep 2, 2022Updated 4 years ago
- Faster multispecies coalescent inference using multilocus data☆15Aug 13, 2023Updated 3 years ago
- 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
- ☆14Dec 15, 2022Updated 3 years ago
- A rust-native port of wfa2lib☆15Aug 1, 2026Updated 3 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- 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 command line tool to manage boring development processes☆10Oct 12, 2026Updated 3 weeks ago
- Source code of the U-TRR methodology presented in "Uncovering In-DRAM RowHammer Protection Mechanisms: A New Methodology, Custom RowHamme…☆19Nov 15, 2022Updated 3 years ago
- SimplePIM is the first high-level programming framework for real-world processing-in-memory (PIM) architectures. Described in the PACT 20…☆40Oct 23, 2023Updated 3 years ago
- SparseP is the first open-source Sparse Matrix Vector Multiplication (SpMV) software package for real-world Processing-In-Memory (PIM) ar…☆79Jun 29, 2022Updated 4 years ago
- ☆12Oct 16, 2026Updated 2 weeks 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