46 citations · 139 across the 15 of their papers we have counts for
6 papers · 1 filter
Rawsamble: Overlapping and Assembling Raw Nanopore Signals using a Hash-based Seeding Mechanism
Can Firtina, Maximilian Mordig, Harun Mustafa +7
Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e., without basecalling).…
MetaTrinity: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation
Arvid E. Gollwitzer, Mohammed Alser, Joel Bergtholdt +5
Metagenomics, the study of genome sequences of diverse organisms cohabiting in a shared environment, has experienced significant advancements across various medical and biological…
RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment
Joël Lindegger, Can Firtina, Nika Mansouri Ghiasi +3
Nanopore sequencers generate raw electrical signals representing the contents of a biological sequence molecule passing through the nanopore. These signals can be analyzed directly…
RawHash2: Mapping Raw Nanopore Signals Using Hash-Based Seeding and Adaptive Quantization
Can Firtina, Melina Soysal, Joël Lindegger +1
Summary: Raw nanopore signals can be analyzed while they are being generated, a process known as real-time analysis. Real-time analysis of raw signals is essential to utilize the u…
RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes
Can Firtina, Nika Mansouri Ghiasi, Joel Lindegger +4
Nanopore sequencers generate electrical raw signals in real-time while sequencing long genomic strands. These raw signals can be analyzed as they are generated, providing an opport…
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser +6
Basecalling is an essential step in nanopore sequencing analysis where the raw signals of nanopore sequencers are converted into nucleotide sequences, i.e., reads. State-of-the-art…