Cover Image

MetaTrinity: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Gollwitzer, Arvid E., Alser, Mohammed, Bergtholdt, Joel, Lindegger, Joel, Rumpf, Maximilian-David, Firtina, Can, Mangul, Serghei, Mutlu, Onur
Format:	Preprint
Published:	2023
Subjects:	Genomics Hardware Architecture Quantitative Methods
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences
by: Rumpf, Maximilian-David, et al.
Published: (2023)

MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing
by: Ghiasi, Nika Mansouri, et al.
Published: (2024)

RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment
by: Lindegger, Joël, et al.
Published: (2023)

RawHash2: Mapping Raw Nanopore Signals Using Hash-Based Seeding and Adaptive Quantization
by: Firtina, Can, et al.
Published: (2023)

GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping
by: Bingöl, Zülal, et al.
Published: (2021)

RUBICON: A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers
by: Singh, Gagandeep, et al.
Published: (2022)

Enabling Fast, Accurate, and Efficient Real-Time Genome Analysis via New Algorithms and Techniques
by: Firtina, Can
Published: (2025)

MARS: Processing-In-Memory Acceleration of Raw Signal Genome Analysis Inside the Storage Subsystem
by: Soysal, Melina, et al.
Published: (2025)

CiMBA: Accelerating Genome Sequencing through On-Device Basecalling via Compute-in-Memory
by: Simon, William Andrew, et al.
Published: (2025)

TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
by: Cavlak, Meryem Banu, et al.
Published: (2022)

Rawsamble: Overlapping and Assembling Raw Nanopore Signals using a Hash-based Seeding Mechanism
by: Firtina, Can, et al.
Published: (2024)

GenPairX: A Hardware-Algorithm Co-Designed Accelerator for Paired-End Read Mapping
by: Eudine, Julien, et al.
Published: (2026)

SAGe: A Lightweight Algorithm-Architecture Co-Design for Mitigating the Data Preparation Bottleneck in Large-Scale Genome Sequence Analysis
by: Ghiasi, Nika Mansouri, et al.
Published: (2025)

Processing-in-memory for genomics workloads
by: Simon, William Andrew, et al.
Published: (2025)

Genome-on-Diet: Taming Large-Scale Genomic Analyses via Sparsified Genomics
by: Alser, Mohammed, et al.
Published: (2022)

Accelerating Seed Location Filtering in DNA Read Mapping Using a Commercial Compute-in-SRAM Architecture
by: Golden, Courtney, et al.
Published: (2024)

AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
by: Kim, Jeremie S., et al.
Published: (2019)

RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques
by: Eris, Furkan, et al.
Published: (2025)

FASTR: Reimagining FASTQ via Compact Image-inspired Representation
by: Tkachenko, Adrian, et al.
Published: (2026)

RowPress Vulnerability in Modern DRAM Chips
by: Luo, Haocong, et al.
Published: (2024)

RowPress: Amplifying Read Disturbance in Modern DRAM Chips
by: Luo, Haocong, et al.
Published: (2023)

NMP-PaK: Near-Memory Processing Acceleration of Scalable De Novo Genome Assembly
by: Kim, Heewoo, et al.
Published: (2025)

Toward Capturing Genetic Epistasis From Multivariate Genome-Wide Association Studies Using Mixed-Precision Kernel Ridge Regression
by: Ltaief, Hatem, et al.
Published: (2024)

A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater
by: Munteanu, Viorel, et al.
Published: (2023)

CRANE: Correcting Errors in Raw Nanopore Signals Using Hidden Markov Models
by: Ambrozak, Simon, et al.
Published: (2026)

CoMeT: Count-Min-Sketch-based Row Tracking to Mitigate RowHammer at Low Cost
by: Bostanci, F. Nisa, et al.
Published: (2024)

Microbial and Viral Ecology Analysis for Metagenomic Data
by: Kosmopoulos, James C., et al.
Published: (2024)

MetaCompass: Reference-guided Assembly of Metagenomes
by: Luan, Tu, et al.
Published: (2024)

Metagenomic analysis revealed significant changes in cattle rectum microbiome and antimicrobial resistome under fescue toxicosis
by: Zhou, Yihang
Published: (2024)

Accelerating Triangle Counting with Real Processing-in-Memory Systems
by: Asquini, Lorenzo, et al.
Published: (2025)

Metagenomic analysis reveals shared and distinguishing features in horse and donkey gut microbiome and maternal resemblance of the microbiota in hybrid equids
by: Zhou, Yihang
Published: (2024)

TPMM: Three-component Posterior Mixture Model Enables Robust Inverton Detection in Low-Depth Metagenomes and Suggests Potential Viral Invertons
by: Lu, Yi, et al.
Published: (2026)

Microbial Mat Metagenomes from Waikite Valley, Aotearoa New Zealand
by: Tauer, Beatrice, et al.
Published: (2024)

Metagenomic Analysis using Phylogenetic Placement -- A Review of the First Decade
by: Czech, Lucas, et al.
Published: (2022)

EasyDRAM: An FPGA-based Infrastructure for Fast and Accurate End-to-End Evaluation of Emerging DRAM Techniques
by: Canpolat, Oğuzhan, et al.
Published: (2025)

Unlocking Noisy Real-World Corpora for Foundation Model Pre-Training via Quality-Aware Tokenization
by: Gollwitzer, Arvid E., et al.
Published: (2026)

PUMA: Efficient and Low-Cost Memory Allocation and Alignment Support for Processing-Using-Memory Architectures
by: Oliveira, Geraldo F., et al.
Published: (2024)

SARS-CoV-2 Wastewater Genomic Surveillance: Approaches, Challenges, and Opportunities
by: Munteanu, Viorel, et al.
Published: (2023)

MetagenBERT: a Transformer-based Architecture using Foundational genomic Large Language Models for novel Metagenome Representation
by: Roy, Gaspar, et al.
Published: (2026)

Memory-Centric Computing: Solving Computing's Memory Problem
by: Mutlu, Onur, et al.
Published: (2025)