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 Bioinformatics.

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.

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.

Assignments in C++