Can Fırtına

RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques

RawBench benchmarks raw nanopore signal analysis techniques, showing they can achieve competitive quality with reduced resource requirements for real-time and edge deployment.

TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering

TargetCall filters out off-target reads before basecalling to reduce computational waste, improving basecalling performance and efficiency.

AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes

AirLift remaps reads from one reference genome to another efficiently and accurately, reducing execution time by up to 27.4x compared to full mapping.

RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes

RawHash enables fast and accurate real-time analysis of nanopore raw signals for large genomes, outperforming existing methods in throughput and accuracy.

BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis

BLEND improves genomic sequence analysis by efficiently finding fuzzy seed matches, enhancing speed, memory use, and accuracy in read overlapping and mapping.

A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers

This paper introduces RUBICON, a framework for designing efficient deep learning-based genomic basecallers, and demonstrates its effectiveness with RUBICALL, a hardware-optimized mixed-precision basecaller that outperforms existing methods.

Hercules: a profile HMM-based hybrid error correction algorithm for long reads

Hercules corrects long read errors using a profile HMM-based machine learning approach, achieving high mapping rates and accuracy when short reads cover most of the long reads.