In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

Yet another k-mer analyzer

SEER, reimplemented in python 🐍🔮

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

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

A compressed, associative, exact, and weighted dictionary for k-mers.

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

A versatile toolkit for k-mers with taxonomic information

Split k-mer analysis – version 2

Remove contaminated contigs from genomes using k-mers and taxonomies.

A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.

Learn interpretable computational phenotyping models from k-merized genomic data

sequence element (kmer) enrichment analysis

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

A Nextflow pipeline for evaluating assembly quality

interactive Multi Objective K-mer Analysis

k-mer similarity analysis pipeline

An RNA virus strain-level identification tool for short reads.