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

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 SIMD-accelerated library to compute random minimizers

Whole chromosome visualization tool

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

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

Accurate, resource-frugal and deterministic DNA sequence classifier.

Bitpacked sequence trait and implementation

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

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

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.

Implementing a complete DeBruijn graph assembly pipeline in R

Statistical comparison and visualization of GC content across species using ANOVA, t-tests, and post-hoc analyses to reveal genomic variation.

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

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

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

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

A compressor for k-mers sets with counters

Phage-Host Interaction Search Tool