kmer based feature extraction tool for bioinformatics, metagenomics, AI/ML and more

A KMER-based genome-wIde Assocation testing approach on polyploids

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

Count kmers with a more efficient (faster) hash table

k-mer similarity analysis pipeline

fast and comprehensive k-mer counting package

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

Parallel String Graph Construction, Transitive Reduction, and Contig Generation for De Novo Genome Assembly

Pangenome openness from k-mers or genes

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

🧮 🔢 Generate multi-sample k-mer count matrix from WGS

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.

Genestrip - Efficient read classification, filtering and k-mer counting for selected groups of species

DNA classifier using Natural Language Processing. Used K-mer method to convert sequence strings into fixed size words

A seed-based homology searching tool

Minimizer counting and analysis

Represents sequences files in fasta format in terms of their kmer counts.

K-mer analysis tools for sequence and structure

STAR Research - Summer '24

This is the Machine learning Project Repo.

fast and lightweight counting of short k-mers

Implementation of k-mer counting algorithms BFCounter and experimental implementation of Misra-Gries. The goal is to use as little memory as possible.

Count canonical kmers with Abseil C++ `absl::flat_hash_map`

Select representative sequencing data sets.

Counting Bloom Filter Algorithm to count kmers

Tools to discover natural selection given multiple evolved DNA sequences (e.g., gnomad cohort, or multiple tumor samples)

A selection of databases for Genestrip

Obtain k-mer counts from fastx files

Kmer counter is written in GO Lang v 1.16.5 To install GO on Windows, follow the instructions at https://golang.org/doc/install 4 GO implementation of N-mer counter in DNA sequences which tests for validity of input. It reads in file name (of fasta file) It reads the size length (kmer length) for which counts are desired and writes out to file, counts of all overlapping kmers of size 1 through the specified input. It checks if fasta file is empty amd whether kmer length is specified.

Counts the number of occurrences of each k-mer in a DNA string