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

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)

Minimizer-based assembly scaffolding and mapping using long reads

Extract kmers, skipmers, minimizers.

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.

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

A collection of minimizer-based sampling algorithms.

Code to create polar sets for genome sketching.

Here we introduce frequency-bounded minimizers - finimizers - for indexing sets of k-mers.

Minimizer counting and analysis

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

Dynamic updates of Minimizers