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

Estimating k-mer coverage histogram of genomics data

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

A quality control tool for FASTQ files written in rust

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

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

fast and comprehensive k-mer counting package

Python bioinformatics CLI for k-mer counts and de Bruijn graphs

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

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

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

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

fast and lightweight counting of short k-mers

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

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.

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.

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

Assignments in C++