38 citations
3 papers
cs.AR2022★ 19 cited
Scrooge: A Fast and Memory-Frugal Genomic Sequence Aligner for CPUs, GPUs, and ASICs
Joël Lindegger, Damla Senol Cali, Mohammed Alser +3
Pairwise sequence alignment is a very time-consuming step in common bioinformatics pipelines. Speeding up this step requires heuristics, efficient implementations, and/or hardware…
cs.AR2022★ 38 cited
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.,…
q-bio.GN2022★ 6 cited
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…