A Nextflow pipeline for evaluating assembly quality

Blazingly fast SRA-scale sequence analysis & QC

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

Split k-mer analysis – version 2

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

SEER, reimplemented in python 🐍🔮

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

PARMIK is a fast and memory-efficient tool for identifying the "Partial Match" region between two genomic sequences.

Polymorphic Edge Detection - An efficient polymorphism detector for NGS data

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

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

Python bioinformatics CLI for k-mer counts and de Bruijn graphs

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

Tools for filtering k-mer data

Detect complete horizontal gene transfer (HGT) event rapidly and accurately from complex metagenomics data.

A versatile toolkit for k-mers with taxonomic information

A java program which identifies and sums all n-grams/shingles/l-mer/k-mer of contiguus size n in a text document, then outputs the results to a file

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

subset and spaced seed design tool

Yet another k-mer analyzer