genome-on-diet

There are 0 repository under genome-on-diet topic.

CMU-SAFARI / Genome-on-Diet
Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).
genome-analysis read-mapping variant-calling containment-search genomics large-scale metagenomic-analysis metagenomics microbiome-analysis sequence-alignment wavefront-alignment bioinformatics minimap2 genome-on-diet
Language:Roff 11
CMU-SAFARI / GateSeeder
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 genome-on-diet genomics hbm indexing long-reads minimap2 minimizers read-mapping seeding sequence-alignment short-reads
Language:C 7

CMU-SAFARI / Genome-on-Diet