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CMU-SAFARI / GateSeeder

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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.

bioinformatics fpga genomics indexing seeding hbm sequence-alignment read-mapping long-reads minimap2 minimizers short-reads genome-on-diet
  • Updated Oct 3, 2023
  • C

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