RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genomes) in real-time without basecalling. Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440).

A speculative mechanism to accelerate long-latency off-chip load requests by removing on-chip cache access latency from their critical path, as described by MICRO 2022 paper by Bera et al. (https://arxiv.org/pdf/2209.00188.pdf)

Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).

DRAM Bender is the first open source DRAM testing infrastructure that can be used to easily and comprehensively test state-of-the-art HBM2 chips and DDR4 modules of different form factors. Six prototypes are available on different FPGA boards. Described in our preprint: https://arxiv.org/pdf/2211.05838.pdf

A new DRAM substrate that mitigates the excessive energy consumption from both (i) transmitting unused data on the memory channel and (ii) activating a disproportionately large number of DRAM cells at low cost. Described in our paper https://arxiv.org/pdf/2207.13795.

MQSim is a fast and accurate simulator modeling the performance of modern multi-queue (MQ) SSDs as well as traditional SATA based SSDs. MQSim faithfully models new high-bandwidth protocol implementations, steady-state SSD conditions, and the full end-to-end latency of requests in modern SSDs. It is described in detail in the FAST 2018 paper by A…

Ramulator 2.0 is a modern, modular, extensible, and fast cycle-accurate DRAM simulator. It provides support for agile implementation and evaluation of new memory system designs (e.g., new DRAM standards, emerging RowHammer mitigation techniques). Described in our paper https://people.inf.ethz.ch/omutlu/pub/Ramulator2_arxiv23.pdf

Rawasm is a patch to the popular miniasm tool. It enables the construction of genome assembly from raw nanopore signals.

A binary instrumentation tool to analyze load instructions in any off-the-shelf x86(-64) program. Described by Bera et al. in https://arxiv.org/pdf/2406.18786

AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shared between the two reference genomes and enables remapping across all parts of the references. Described by Kim et al. (preliminary version at http://arxiv.org/abs/1912.08735)