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kmers

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jermp /fulgor

Fulgor is a fast and space-efficient colored de Bruijn graph index.

hashing bioinformatics de-bruijn-graphs kmers

UpdatedFeb 26, 2025
C++

akcorut /kGWASflow

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

workflow bioinformatics gwas snakemake pipeline genomics ngs conda bioinformatics-pipeline structural-variation gwas-pipeline bioinformatics-tool gwas-tools kmers sciworkflows association-mapping

UpdatedApr 18, 2024
Python

suchapalaver /krust

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

rust bioinformatics genomics bytes parallelization beginner-friendly kmer k-mer insta k-mer-counting clap rayon kmer-counting bioinformatics-tool kmers k-mers bitpacking rust-bio dashmap needletail

UpdatedSep 25, 2023
Rust

Discount

jtnystrom /Discount

Very large scale k-mer counting and analysis on Apache Spark.

bioinformatics scala spark genomics kmer-frequency-count kmer-counting kmers

UpdatedFeb 9, 2024
Scala

slowikj /seqR

fast and comprehensive k-mer counting package

hashing bioinformatics rcpp genomics feature-extraction protein-sequences ngram ngrams kmer k-mer feature-engineering hashing-algorithms k-mer-counting kmer-frequency-count kmer-counting rpackage bioinformatics-tool kmers rcppparallel dna-processing

UpdatedSep 27, 2021
C++

arminZolfaghari /DNA-Sequence-Classification

Analysis of DNA Sequence Classification Using Neural Networks - Bioinformatics Course Project - Winter 2022

bioinformatics deep-learning dna classification word-embedding dna-sequence-analysis kmers dna-analysis

UpdatedNov 13, 2023
Jupyter Notebook

OndrejSladky /kmercamel

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

bioinformatics genomics bioinformatics-tool kmers k-mers masked-superstrings

UpdatedMar 5, 2025
C++

hannesbecher /shiny-k-mers

Tetemer, an R package and Shiny app for interactively fitting population parameters to k-mer spectra of diploids, triploids, and tetraploids (allo and auto)

bioinformatics genome-size polyploidy kmers k-mers k-mer-spectrum allotetraploidy tetmer ploidy-inference

UpdatedAug 14, 2024
R

BioJulia /KmerAnalysis.jl

K-mer counting algorithms and count-data utilities for the BioJulia framework

kmer kmer-frequency-count kmer-distribution kmer-counting biojulia kmer-composition kmers kmer-spectra

UpdatedApr 23, 2023
Julia

dib-lab /kmerDecoder

Extract kmers, skipmers, minimizers.

kmers skipmers skip-mers minimizers

UpdatedMay 24, 2024
C++

bioinfoUQAM /CASTOR_KRFE

Alignment-free method to identify and analyse discriminant genomic subsequences within pathogen sequences

machine-learning svm feature-extraction alignment-free castor taxonomic-classification kmers rfe virus-classification castor-krfe svm-rfe

UpdatedFeb 26, 2023
Python

suchapalaver /fastas2kmers

A naive implementation of a k-mer counter in Python, takes fasta files and k-mer length requests and outputs all k-mers of length k, their reverse complement, and their frequency within their respective sequence for each sequence in the file.

kmer fasta-sequences kmer-frequency-count kmer-counting fasta-format kmers kmer-length

UpdatedMar 28, 2022
Python

shenwei356 /kmers

bit-packed k-mers methods for Golang

UpdatedNov 14, 2023
Go

phylo42 /RAPPAS

Rapid, Alignment-free, Phylogenetic Placement via Ancestral Sequences

metagenomics phylogenetics metabarcoding placement taxonomic-classification phylogenetic-placement kmers phylo-kmers genetic-markers

UpdatedDec 20, 2023
Java

phylo42 /sherpas

Screening Historical Events of Recombination in a Phylogeny via Ancestral Sequences

virus recombination subtyping genotyping kmers ancestral-sequences phylo-kmers recombination-detection

UpdatedJan 12, 2021
C++

moorembioinfo /KmerAperture

Extract SNPs and accessory differences in closely related bacterial genomes from k-mers

snps genomics alignment-free kmers

UpdatedJan 6, 2024
Python

kcleal /kmerhash

Convert python string to hashed kmers and back again

bioinformatics hash kmer kmers

UpdatedJul 21, 2023
Cython

GioStamoulos /Kmers_Dataset_Generation_Regression_Clustering

The generation of a kmers dataset that is associated with multiple gene sequences and the further manipulation of this generated dataset are the main contents of the current project.

machine-learning bioinformatics genomics clustering sklearn regression computational-biology pandas matplotlib kmeans blast data-manipulation isomap svr kmers data-harvesting

UpdatedJan 11, 2022
Jupyter Notebook

adamjorr /kbbq

reference-free base quality score recalibration

bioinformatics genomics htslib fastq kmers

UpdatedOct 16, 2020
C++

polyglotDataNerd /poly-spark-kmers

bioinformatics scala spark kmers

UpdatedApr 26, 2021
Scala

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