Code examples of fast and simple k-mer counters for tutorial purposes

Estimating k-mer coverage histogram of genomics data

A quality control tool for FASTQ files written in rust

find large indels (in the blind spot between GATK/freebayes and SV callers)

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

fast and comprehensive k-mer counting package

MerCat: python code for versatile k-mer counting and diversity estimation for database independent property analysis for meta -ome data

MerCat2: python code for versatile k-mer counting and diversity estimation for database independent property analysis for metaome data

Python CLI for alignment-free genomics.

A k-mer counter that streams gene-cluster specific k-mers, while keeping k-mer positional information. Useful for microbial GWAS analyses with higher interpretability.

K-mer indexing and querying in RNA-Seq data

A specialized datastructure for counting short DNA sequences for use in Machine Learning and Bioinformatics.

Get Started with DNA Sequencing working with .FastQ and .FastA file formats and performing Pattern Matching Algorithms (Exact & Approximate).

fast and lightweight counting of short k-mers

A PHP hash table optimized for counting short gene sequences for use in Bioinformatics.

Multi-Level Taxonomic Novelty Detection with Increased Genomic Depth

Utilizing support vector machines, naïve bayes classification and neural networks to find which gives the best results of classification of DNA sequence data into 7 different protein classes.

Implementación del algoritmo para contar K-mers en una secuencia genética usando GPUs.

A project submitted as the requirement of the course CSE 549 (Computational Biology), titled as "Efficient Parallelization for KmerEstimate: A Streaming Algorithm for Estimating k-mer Counts with Optimal Space Usage". Original serial algorithm available at github.com/srbehera11/KmerEstimate.