minimizers

There are 11 repositories under minimizers topic.

  • 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:Python9247113

  • 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:C421264

  • bcgsc/ntLink

    Minimizer-based assembly scaffolding and mapping using long reads

    Language:Python329127

  • dib-lab/kmerDecoder

    Extract kmers, skipmers, minimizers.

    Language:C++105323

  • 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:C8600

  • ITBE-Lab/seed-evaluation

    Evaluation tools for "A performant bridge between fixed-size and variable-size seeding"

    Language:Python6201

  • jermp/minimizers

    A collection of minimizer-based sampling algorithms.

    Language:C++6211

  • Kingsford-Group/polarset

    Code to create polar sets for genome sketching.

    Language:Python640

  • at-cg/MMC

    Minimizer counting and analysis

    Language:C++2101

  • aljpetri/DynamicMinimizer

    Dynamic updates of Minimizers

    Language:C++0000

  • joao-conde/fer-bio

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

    Language:C++0000