Indexing & querying large assembly graphs -- in space, no one can hear you miao!

A method for variant graph genotyping based on exact alignment of k-mers

COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)

A Rust library providing fully dynamic sets of k-mers with high locality

Fast and compact locality-preserving minimal perfect hashing for k-mer sets.

High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers

Accurate, resource-frugal and deterministic DNA sequence classifier.

Bioinformatics 101 tool for counting unique k-length substrings in DNA

Phage-Host Interaction Search Tool

ProphAsm – a rapid computation of simplitigs directly from k-mer sets

Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)

Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)

Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]

KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.

Tetemer, an R package and Shiny app for interactively fitting population parameters to k-mer spectra of diploids, triploids, and tetraploids (allo and auto)

A k-mer counter that streams gene-cluster specific k-mers, while keeping k-mer positional information. Useful for microbial GWAS analyses with higher interpretability.

simple virus DNA classification

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

ProPhex – an exact k-mer index using Burrows-Wheeler Transform

Investigating genome size variation with k-mers