About Humanomics

Humanomics is a comprehensive software pipeline developed by the Bioinformatics (BIF) group at CHU Liège, designed for the detection of genetic variations—specifically single nucleotide polymorphisms (SNPs) and insertions or deletions (INDELs)—from short-read high-throughput DNA sequencing data. This tool is instrumental for researchers and clinicians aiming to elucidate the genetic underpinnings of various human health conditions and diseases. It is used for patient diagnostic at the CHU Liège, in a workflow under ISO-15189.

Purpose and Functionality :

In the realm of genomics, accurately identifying SNPs and INDELs is paramount, as these genetic variations can significantly influence an individual's susceptibility to diseases, response to medications, and other health-related traits. Humanomics addresses this need by providing a streamlined and efficient pipeline that processes raw sequencing data to infer these variations with high sensitivity and precision. By automating and integrating various analytical steps, Humanomics reduces the complexity and time required for genomic analysis, thereby accelerating research and potential clinical applications.

Key Features:

• Automated Workflow: Humanomics integrates multiple stages of data processing—from quality control and alignment to variant calling—into a cohesive pipeline, minimizing manual intervention and potential errors.
• Open-Source Accessibility: Distributed under the GNU Affero General Public License version 3 (AGPLv3), Humanomics encourages collaboration and transparency. Users are free to use, modify, and distribute the software, provided that any derivative works adhere to the same licensing terms.
• Versatile Development: The software is primarily developed in Python, known for its readability and extensive libraries, with additional components in Scala and Shell scripting. This combination ensures both performance efficiency and ease of customization.
• Command-Line Interface (CLI): Humanomics operates through a command-line interface, offering advanced users the flexibility to integrate the tool into larger automated workflows and customize analyses to their specific needs.

Applications:

Humanomics is particularly valuable in various applications, including:

• Medical Research: Identifying genetic markers associated with diseases to advance understanding and development of targeted therapies.
• Pharmacogenomics: Analyzing genetic variations that affect individual responses to drugs, aiding in personalized medicine approaches.
• Population Genetics: Studying genetic diversity and evolutionary patterns within and between populations.

By providing a reliable and efficient tool for variant detection, Humanomics contributes significantly to the fields of genomics and personalized medicine, enabling more precise and informed health interventions.

For more detailed information, access to the source code, and contribution guidelines, please visit the Humanomics GitLab repository.

Authors

Benoît Charloteaux (CHU Liège)

Laura Helou (CHU Liège)

Lennart C. Karssen (PolyOmica)

Maarten Kooijman (Oyat Consulting)

Leonor Palmeira (CHU Liège)

Lauriane Paquet

Christophe Russo (CHU Lille)

Ines Sonet

WEBSITE

Reference Publication