5 papers
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…
SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences
Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer +5
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational…
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…
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…