In-depth data movement characterization of DNA read mapping algorithms

arXiv:2611.03400v1 Announce Type: new Abstract: Read mapping algorithms represent a critical bottleneck in genomic analysis pipelines due to the resources required; a problem that is becoming more pronounced as sequencing technologies advance and datasets expand. We present an extensive workload characterization of leading read mapping algorithms across diverse sequencing technologies to identify hardware acceleration and optimization opportunities. We analyzed the following implementations: MashMap, wfmash, and Minimap2 for whole-genome alignment (WGA); NGMLR, Minimap2, and LRA for long reads; and Bowtie2, BWA-MEM, StrobeAlign, and minibwa for short reads.