Skip to content
#

genome-on-diet

Star

Here are 3 public repositories matching this topic...

Language: All
Filter by language
All 3 C 1 Roff 1 Java 1

CMU-SAFARI / Genome-on-Diet

Star 11

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).

bioinformatics genomics metagenomics variant-calling containment-search genome-analysis large-scale sequence-alignment read-mapping metagenomic-analysis microbiome-analysis minimap2 wavefront-alignment genome-on-diet
  • Updated Sep 4, 2024
  • Roff

CMU-SAFARI / GateSeeder

Star 8

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

Improve this page

Add a description, image, and links to the genome-on-diet topic page so that developers can more easily learn about it.

Curate this topic

Add this topic to your repo

To associate your repository with the genome-on-diet topic, visit your repo's landing page and select "manage topics."

Learn more