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Found 14 papers, 13 papers with code
MetaTrinity: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation
This dual comparison positions MetaTrinity as a broadly applicable solution for metagenomic classification, combining advantages of both ends of the spectrum: speed and accuracy.
SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences
Comparing genomic sequences is one of the most fundamental computational steps in most genomic analyses.
RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment
mean) while improving accuracy by 1. 35$\times$ (1. 34$\times$) in terms of F-1 score on average (geo.
RawHash2: Accurate and Fast Mapping of Raw Nanopore Signals using a Hash-based Seeding Mechanism
Summary: Raw nanopore signals can be analyzed while they are being generated, a process known as real-time analysis.
RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes
RawHash achieves an accurate hash-based similarity search via an effective quantization of the raw signals such that signals corresponding to the same DNA content have the same quantized value and, subsequently, the same hash value.
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
However, for many applications, the majority of reads do no match the reference genome of interest (i. e., target reference) and thus are discarded in later steps in the genomics pipeline, wasting the basecalling computation.
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis
We identify an urgent need for a flexible, high-performance, and energy-efficient HW/SW co-design to address the major inefficiencies in the Baum-Welch algorithm for pHMMs.
Going From Molecules to Genomic Variations to Scientific Discovery: Intelligent Algorithms and Architectures for Intelligent Genome Analysis
We hope that these efforts and the challenges we discuss provide a foundation for future work in making genome analysis more intelligent.
Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities
Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research.
FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies
Also available in Bioconda at: https://anaconda. org/bioconda/fastremap-bio.
BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis
We introduce BLEND, the first efficient and accurate mechanism that can identify both exact-matching and highly similar seeds with a single lookup of their hash values, called fuzzy seed matches.
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis
Unfortunately, it is currently bottlenecked by the computational power and memory bandwidth limitations of existing systems, as many of the steps in genome sequence analysis must process a large amount of data.
Hardware Architecture Genomics
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
There are several tools that attempt to accelerate the process of updating a read data set from one reference to another (i. e., remapping).
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
Our experiments with real read sets demonstrate that Apollo is the only algorithm that 1) uses reads from any sequencing technology within a single run and 2) scales well to polish large assemblies without splitting the assembly into multiple parts.
