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GitHub topics: genome-on-diet

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.

Language: C - Size: 1.24 MB - Last synced at: 12 months ago - Pushed at: almost 2 years ago - Stars: 7 - Forks: 0

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).

Language: Roff - Size: 63 MB - Last synced at: 12 months ago - Pushed at: almost 2 years ago - Stars: 11 - Forks: 4

Related Keywords
bioinformatics 2 genome-on-diet 2 genomics 2 minimap2 2 read-mapping 2 sequence-alignment 2 wavefront-alignment 1 variant-calling 1 microbiome-analysis 1 metagenomics 1 metagenomic-analysis 1 large-scale 1 genome-analysis 1 containment-search 1 short-reads 1 seeding 1 minimizers 1 long-reads 1 indexing 1 hbm 1 fpga 1