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GitHub topics: minimizers

Repositories

jermp/minimizers

A collection of minimizer-based sampling algorithms.

Language: C++ - Size: 0 Bytes - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 1 - Forks: 0

bcgsc/ntLink

Minimizer-based assembly scaffolding and mapping using long reads

Language: Python - Size: 12.3 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 27 - Forks: 7

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: about 2 months ago - Pushed: about 1 year ago - Stars: 34 - Forks: 3

joao-conde/fer-bio

Repository to host the project for "Bioinformatics", a course @ FER

Language: C++ - Size: 1.45 MB - Last synced: about 2 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

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: 4 months ago - Pushed: 4 months ago - Stars: 76 - Forks: 12

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: about 2 months ago - Pushed: 8 months ago - Stars: 5 - Forks: 0