GitHub - gkanogiannis/BioInfoJava-Utils: BioInfoJava-Utils (original) (raw)

BioInfoJava-Utils

BioInfoJava-Utils is a modular Java library providing high-performance implementations of core bioinformatics algorithms, such as distance matrix computation and phylogenetic tree construction from VCF and FASTA files.

This library serves as the computational backend for the fastreeR software suite, which offers a flexible and user-friendly interface to these tools across multiple platforms and environments.

Integration and Accessibility

The functionality of BioInfoJava-Utils is exposed through the fastreeR interface, which is accessible in the following ways:

Overview

BioInfoJava-Utils provides efficient, scalable, and parallel implementations of widely used bioinformatics algorithms. It is designed for processing large-scale genomic datasets efficiently, supporting both research and production environments.

Features

Installation

Prerequisites

Building from Source

  1. Clone the repository:

    git clone https://github.com/gkanogiannis/BioInfoJava-Utils.git

  2. Navigate to the project directory:

  3. Build the project using Maven:

    mvn clean package install

This will generate a JAR files in the bin directory.

Usage

The main class for executing the utilities is:

com.gkano.bioinfo.javautils.JavaUtils

You can run the utilities via the command line or integrate them into other Java applications.

java -jar bin/BioInfoJavaUtils-VERSION-jar-with-dependencies.jar --help

License

This project is licensed under the GNU General Public License v3.0.

Citation

If you use BioInfoJava-Utils in your research, please cite the following:

Gkanogiannis, A. et al. A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes. BMC Bioinformatics 17, 311 (2016). https://doi.org/10.1186/s12859-016-1186-3

Author

Anestis Gkanogiannis
Bioinformatics/ML Scientist
Website: https://www.gkanogiannis.com
ORCID: 0000-0002-6441-0688