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

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

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

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

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

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

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

A SIMD-accelerated library to compute random minimizers

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

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

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

Bitpacked sequence trait and implementation

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.

Alignment-free phylogenomic splits

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

Quick k-mer-based FASTA/FASTQ sequence record extraction, and SAM/BAM record filtering plus file annotation with k-mer tags.

Investigating genome size variation with k-mers

Supplementary repository for "Efficient and robust search of microbial genomes via Phylogenetic Compression"

web application for DNA comparison, alignment and phylogenetic tree. Released on 2020.

Get Started with DNA Sequencing working with .FastQ and .FastA file formats and performing Pattern Matching Algorithms (Exact & Approximate).

BioSet2Vec is a tool designed to extract k-mer dictionaries from multiple sets of biological sequences using distributed computing. This method is efficient for large-scale biological sequence analysis, enabling users to handle diverse sequence sets, such as DNA sequences, and extract k-mer representations in a distributed fashion.

A compressor for k-mers sets with counters

Minimiser-based digital normalisation for long-read DNA sequence datasets