PlantOmicsGwas 0.1.3

Integrated GWAS and genomic prediction pipeline with a GUI for plant genomics.

PlantOmicsGwas: An Integrated GWAS and Genomic Prediction Pipeline for Plant Genomes

Developers & Contributors

Developer	Expertise
Ahmed Yassin	Computational Biologist
Falak Sher Khan	Computational Biologist
PlantOmicsGwas Software (Affiliation)	Ye-Lab (PKU-IAAS)
PlantOmicsGwas Status	Early Demonstration Release (Under Active Development)

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Developed By:

• Ahmed Yassin, Computational Biologist || PhD Candidate
• Falak Sher Khan, PhD, computational biologist The Peking university of Advanced Agricultural Science (PKU-IAAS), China

⚠️ Early Demonstration Release (v0.1.3)

PlantOmicsGwas v0.1.0 is the first public demonstration release of the software and is intended exclusively for evaluation, testing, and feedback from researchers, collaborators, and the plant genomics community.

The platform is currently under active development. Although the core analytical workflow is functional, we are continuously improving computational performance, large-scale genomic data processing, workflow efficiency, the graphical user interface, and the overall user experience.

Following the publication of our accompanying research manuscript, we will release the complete production version of PlantOmicsGwas, including comprehensive documentation, finalized software licensing, detailed installation guides, tutorials, and the full implementation of all planned analytical modules.

We sincerely appreciate feedback from researchers and early adopters, as it will play an important role in the continued refinement and development of the platform.

Quick Installation (Linux)

PlantOmicsGwas depends on several external bioinformatics tools in addition to the Python package. Please follow the steps below to install all required components.

Step 1 — Install Miniforge (Conda)

Download and install Miniforge:

wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh

bash Miniforge3-Linux-x86_64.sh

source ~/.bashrc

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Step 2 — Create the PlantOmicsGwas Environment

Create a dedicated Conda environment and install all required bioinformatics dependencies.

mamba create -n plantomicsgwas \
-c conda-forge \
-c bioconda \
python=3.11 \
samtools \
bcftools \
bowtie2 \
minimap2 \
plink \
-y

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Step 3 — Activate the Environment

conda activate plantomicsgwas

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Step 4 — Install PlantOmicsGwas

Install the latest release from PyPI together with all optional modules.

pip install --upgrade pip

pip install plantomicsgwas

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Step 5 — Launch PlantOmicsGwas

Start the graphical user interface.

plantomicsgwas-gui

Alternatively, launch the command-line interface.

plantomicsgwas --help

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Verify Installation

Verify that all required bioinformatics tools are correctly installed.

samtools --version
bcftools --version
bowtie2 --version
minimap2 --version
plink --version

If all commands return their version numbers without errors, PlantOmicsGwas has been installed successfully and is ready for use.