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GateSeeder is the first near-memory CPU-FPGA co-design for alleviating both the compute-bound and memory-bound bottlenecks in short and long-read mapping. GateSeeder outperforms Minimap2 by up to 40.3×, 4.8×, and 2.3× when mapping real ONT, HiFi, and Illumina reads, respectively.

Makefile 2.81% Tcl 0.48% Rust 2.38% C++ 34.28% Gnuplot 6.42% Shell 4.80% Awk 0.31% C 48.52%
bioinformatics fpga genome-on-diet genomics hbm indexing long-reads minimap2 minimizers read-mapping

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