A Streaming Algorithm for Estimating k-mer Counts with Optimal Space Usage in Parallel

(dockerized) dna2vec: Consistent vector representations of variable-length k-mers

jellyfish wrapper to extract unique kmers in fasta file compared to background set

A seed-based homology searching tool

A program to read sequences from fastq file and find out the frequency of all substrings with length k across all sequences in the file.

Context aware Move To Front Transform based compressor

Counts k-kmers and sorts top "k" kmer by occurrence.

A k-mer serialization package for Golang

Count canonical kmers with Emil Ernerfeldt's emilib::HashMap

Collapse a set of redundant kmers to use IUPAC degenerate bases

This is our implementation for D2 distance algorithm for k-mers.

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.

ALTEMO is a package of functions written in Python for bioinformatics proposed as a final project in the course of Algorithmic Techniques and Models (325) at the University of Málaga.

Decompose a k-mer profile into several peaks each representing a copy number.

Scripts for Hill et al. (2025) doi:10.1093/g3journal/jkaf082 🚀

Sub Cellular Localisation Prediction

A C and Python implementation of latent strain analysis for eigengenome partitioning.

Count canonical kmers with STL unordered_map

instructions, python and R code for generating lava lamp plots of kmer coverage