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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.
- 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.
- Python Binding: You can import kmertools functionality using
import pykmertools as kt
You can install kmertools from Bioconda at https://anaconda.org/bioconda/kmertools. Make sure you have conda installed.
# create conda environment and install kmertools
conda create -n kmertools -c bioconda kmertools
# activate environment
conda activate kmertoolsYou can install kmertools from PyPI at https://pypi.org/project/pykmertools/.
pip install pykmertoolsYou 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 --releaseNow 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:$(pwd)/target/release/" >> ~/.bashrc
source ~/.bashrc
# to save to ~/.zshrc for Mac
echo "export PATH=\$PATH:$(pwd)/target/release/" >> ~/.zshrc
source ~/.zshrcTo install the python bindings run the following commands. You can use either pip or conda directories for this.
# pip
cd pip
maturin build --release
# conda
cd conda
maturin build --releaseNow move to parent directory using cd .. and run the following command.
pip install target/wheels/pykmertools-<VERSION>-cp39-abi3-manylinux_2_34_x86_64.whlAfter setting up, run the following command to print out the kmertools help message.
kmertools --helpPlease read our comprehensive Wiki.
- Anuradha Wickramarachchi https://anuradhawick.com
- Vijini Mallawaarachchi https://vijinimallawaarachchi.com
If you use kmertools please cite as follows.
@software{Wickramarachchi_kmertools_DNA_Vectorisation,
author = {Wickramarachchi, Anuradha and Mallawaarachchi, Vijini},
title = {{kmertools: DNA Vectorisation Tool}},
url = {https://github.com/anuradhawick/kmertools},
version = {0.1.4}
}Please refer to the Wiki for citations of relevant algorithms.
Please get in touch via author websites or GitHub issues. Thanks!