GitHub topics: minimizers
rust-seq/simd-minimizers
A SIMD-accelerated library to compute random minimizers
Language: Rust - Size: 4.92 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 18 - Forks: 4
bcgsc/ntLink
Minimizer-based assembly scaffolding and mapping using long reads
Language: Python - Size: 12.3 MB - Last synced at: 17 days ago - Pushed at: 7 months ago - Stars: 39 - Forks: 7
ElenaBiagi/Finito
Here we introduce frequency-bounded minimizers - finimizers - for indexing sets of k-mers.
Language: C++ - Size: 389 KB - Last synced at: 30 days ago - Pushed at: 30 days ago - Stars: 9 - Forks: 1
pirovc/ganon
ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
Language: Python - Size: 24.2 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 96 - Forks: 12
CMU-SAFARI/BLEND
BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGAB https://doi.org/10.1093/nargab/lqad004)
Language: C - Size: 13.6 MB - Last synced at: 1 day ago - Pushed at: about 2 years ago - Stars: 43 - Forks: 4
jermp/minimizers
A collection of minimizer-based sampling algorithms.
Language: C++ - Size: 69.3 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 5 - Forks: 1
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: 10 months ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 0
Kingsford-Group/polarset
Code to create polar sets for genome sketching.
Language: Python - Size: 44.9 KB - Last synced at: 8 months ago - Pushed at: over 4 years ago - Stars: 6 - Forks: 0
dib-lab/kmerDecoder
Extract kmers, skipmers, minimizers.
Language: C++ - Size: 584 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 9 - Forks: 3
at-cg/MMC
Minimizer counting and analysis
Language: C++ - Size: 4.56 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1
ITBE-Lab/seed-evaluation
Evaluation tools for "A performant bridge between fixed-size and variable-size seeding"
Language: Python - Size: 136 KB - Last synced at: 2 months ago - Pushed at: over 4 years ago - Stars: 6 - Forks: 1
aljpetri/DynamicMinimizer Fork of xxsds/DYNAMIC
Dynamic updates of Minimizers
Language: C++ - Size: 37 MB - Last synced at: 7 months ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
joao-conde/fer-bio
Repository to host the project for "Bioinformatics", a course @ FER
Language: C++ - Size: 1.45 MB - Last synced at: 3 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
