kmertools: DNA Vectorisation Tool

$$\   $$\                                   $$$$$$$$\                     $$\           
$$ | $$  |                                  \__$$  __|                    $$ |          
$$ |$$  / $$$$$$\$$$$\   $$$$$$\   $$$$$$\     $$ |    $$$$$$\   $$$$$$\  $$ | $$$$$$$\ 
$$$$$  /  $$  _$$  _$$\ $$  __$$\ $$  __$$\    $$ |   $$  __$$\ $$  __$$\ $$ |$$  _____|
$$  $$<   $$ / $$ / $$ |$$$$$$$$ |$$ |  \__|   $$ |   $$ /  $$ |$$ /  $$ |$$ |\$$$$$$\  
$$ |\$$\  $$ | $$ | $$ |$$   ____|$$ |         $$ |   $$ |  $$ |$$ |  $$ |$$ | \____$$\ 
$$ | \$$\ $$ | $$ | $$ |\$$$$$$$\ $$ |         $$ |   \$$$$$$  |\$$$$$$  |$$ |$$$$$$$  |
\__|  \__|\__| \__| \__| \_______|\__|         \__|    \______/  \______/ \__|\_______/ 

Overview

kmertools is a k-mer based feature extraction tool designed to support metagenomics and other bioinformatics analytics. This tool leverages k-mer analysis to vectorize DNA sequences, facilitating the use of these vectors in various AI/ML applications.

Features

• Oligonucleotide Frequency Vectors: Generate frequency vectors for oligonucleotides.
• Minimiser Binning: Efficiently bin sequences using minimisers to reduce data complexity.
• Chaos Game Representation (CGR): Compute CGR vectors for DNA sequences based on k-mers or whole sequence transformation.
• Coverage Histograms: Create coverage histograms to analyze the depth of sequencing reads.

Installation

You can install kmertools directly from the source by cloning the repository and using Rust's package manager cargo.

git clone https://github.com/your-repository/kmertools.git
cd kmertools
cargo build --release

Now add the binary to path (you may modify ~/.bashrc or ~/.zshrc)

# to add to current terminal
export PATH=$PATH:$(pwd)/target/release/
# to save to ~/.bashrc
echo "export PATH=\$PATH:$(pwd)/target/release/" >> ~/.bashrc
# to save to ~/.zshrc
echo "export PATH=\$PATH:$(pwd)/target/release/" >> ~/.zshrc

Help

Please read our comprehensive Wiki.

Authors

• Anuradha Wickramarachchi https://anuradhawick.com
• Vijini Mallawaarachchi https://vijinimallawaarachchi.com

Support and contributions

Please get in touch via author websites or GitHub issues. Thanks!