46 citations · 107 across the 9 of their papers we have counts for
5 papers · 1 filter
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…
RUBICON: A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers
Gagandeep Singh, Mohammed Alser, Kristof Denolf +5
Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide bases using a computational step called basecalling. The a…
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis
Can Firtina, Kamlesh Pillai, Gurpreet S. Kalsi +10
Profile hidden Markov models (pHMMs) are widely employed in various bioinformatics applications to identify similarities between biological sequences, such as DNA or protein sequen…
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping
Damla Senol Cali, Konstantinos Kanellopoulos, Joel Lindegger +15
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e.,…
FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak +3
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a…