k-mer
There are 67 repositories under k-mer topic.
dib-lab/khmer
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
bluenote-1577/sylph
ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
steineggerlab/Metabuli
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
lh3/yak
Yet another k-mer analyzer
mgalardini/pyseer
SEER, reimplemented in python 🐍🔮
pirovc/ganon
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
bacpop/PopPUNK
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
bacpop/ska.rust
Split k-mer analysis – version 2
refresh-bio/kmer-db
Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).
jermp/sshash
📖 🧬 SSHash is a compressed, associative, exact, and weighted dictionary for k-mers.
shenwei356/unikmer
A versatile toolkit for k-mers with taxonomic information
dib-lab/charcoal
Remove contaminated contigs from genomes using k-mers and taxonomies.
aldro61/kover
Learn interpretable computational phenotyping models from k-merized genomic data
seqan/raptor
A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.
johnlees/seer
sequence element (kmer) enrichment analysis
Plant-Food-Research-Open/assemblyqc
A Nextflow pipeline for evaluating assembly quality
suchapalaver/krust
Bioinformatics 101 tool for counting unique k-length substrings in DNA
nf-core/kmermaid
k-mer similarity analysis pipeline
RitchieLabIGH/iMOKA
interactive Multi Objective K-mer Analysis
Sh1ne111/KMERIA
A KMER-based genome-wIde Assocation testing approach on polyploids
liaoherui/VirStrain
An RNA virus strain-level identification tool for short reads.
slowikj/seqR
fast and comprehensive k-mer counting package
mbhall88/skc
Shared k-mer content between two genomes
deepomicslab/LocalHGT
Detect complete horizontal gene transfer (HGT) event rapidly and accurately from complex metagenomics data.
bacpop/sketchlib.rust
Fast sequence distance estimates
MatthewRalston/kmerdb
Python CLI for alignment-free genomics.
ElenaBiagi/Finito
Here we introduce frequency-bounded minimizers - finimizers - for indexing sets of k-mers.
WCSCourses/K-mer_Biodiversity_Genomics_2025
Introduction and advanced uses of k-mers in biodiversity genomics using modern k-mer tools and methods.
berybox/KEC
Unique sequence search by K-mer exclusion
bioinfo-ut/AluMine
Scripts for discovery and genotyping polymorphic Alu element insertions in human genomes
CamilaDuitama/aKmerBroom
🧹🦷 aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets
luffy563/circRNA_tools_comparison
This repository contains the results and comparison visualization of circRNA candidates detected by circRNA prediction softwares.
pmenzel/kiq
K-mer indexing and querying in RNA-Seq data
tobiasrausch/rdxon
Reference-free FASTQ filter for rare germline and somatic variants
CamilaDuitama/decOM
🗑️🦷 decOM 🦷🗑️
zmmason/BINF
Computational programs and algorithms used to convert information from biochemical experiments (DNA/RNA/Protein/DNA chip/NGS) into useful information and data.