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anmlzoo

High-performance automata-processing engines are traditionally evaluated using a limited set of regular expression rulesets. While regular expression rulesets are valid real-world examples of use cases for automata processing, they represent a small proportion of all use cases for automata-based computing. With the recent availability of architectures and software frameworks for automata processing, many new applications have been found to benefit from automata processing. These show a wide variety of characteristics that differ from prior, popular regular-expression benchmarks, and these should be considered when designing new systems for automata processing. This paper presents ANMLZoo, a benchmark repository for automata-based applications as well as automata engines for both von-Neumann and reconfigurable data flow architectures.

anmlzoo_apprng

apprng

automata-to-routing

automatalab

Visualization web client for VASim

bonito

Bonito - A PyTorch Basecaller for Oxford Nanopore Reads

eecs-498-598-hw2

github-clone-scraper

Python script that scrapes GitHub repositories to keep track of total clone counts. This is useful for projects that are NSF funded, where "impact" (total downloads) is required to be reported.

gpu-programming-assignment

graphgrep

hyperscan

High-performance regular expression matching library

kraken

Kraken taxonomic sequence classification system

kraken2

The second version of the Kraken taxonomic sequence classification system

lamprey

A Loop-Mediated Isothermal Amplification (LAMP) concatemer analysis, variant calling, and polishing tool

lava-dna

LAVA (LAMP Assay Versatile Analysis) is an extendable open-source Loop-mediated isothermal AMPlification (LAMP)

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

mncart

MNRL Network Computation and Research Testbed

mnrl

MNRL Network Representation Language

swalign

Smith-Waterman local aligner

taiyaki

Training models for basecalling Oxford Nanopore reads

ultrarapidseq

This repository is meant to accompany the paper "Ultra-rapid Sequencing-based Molecular Diagnostics via Real-Time Threshold Sequencing." It is a collection of scripts used to perform certain analysis from the paper, and shared for reproducibility.

vasim

VASim is a virtual homogeneous non-deterministic finite automata automata simulator and transformation tool. VASim can parse, transform, simulate, and profile homogeneous NFAs, and is meant to be an open tool for automata processing research. VASim can also be extended to support hypothetical automata processing elements.