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T-Rex: Desktop App for TRIO WES Rare Variant Analysis Overview T-Rex (Trio Rare variant analysis of Exomes) is a desktop application for standardized and local analysis of Illumina whole-exome sequencing germline trio data. It enables users to process FASTQ, BAM, VCF, CSV, and TSV files with customizable filtering options for variant type, statistical significance, and population allele frequency based on the gnomAD database. Key Features • Intuitive desktop GUI built with CustomTkinter (Python)• Compatible with macOS (arm64), Linux (x86, Ubuntu ≥24), and Windows (via WSL2 on Windows 11+)• End-to-end integrated analysis pipeline with: o Read preprocessing using Trimmomatic o Alignment to GRCh38 reference genome using BWA-MEM o Post-processing with Picard o Variant calling by GATK4 HaplotypeCaller and VarScan2 o Variant annotation via SnpEff / SnpSift o Quality control after each analysis step• Statistical tests supported: Chi-square test and Transmission Disequilibrium Test with automatic Bonferroni correction (α ≤ 0.05)• Filtering based on allele frequency from gnomAD v4.0 (European population >582,716 individuals)• Pathogenicity annotation using ClinVar data• Tested with 13 medical doctors and scientists for stability and intuitive user design Getting Started System Requirements • macOS: arm64 (M1+ chips)• Linux: x86 architecture (Ubuntu 24+)• Windows: Windows 11 with WSL2 enabled (see official WSL installation guide)• The app was tested on M1 chips and on Ubuntu 24. Installation Running T-Rex on macOS 1. Download T-Rex-macos-arm64.zip. 2. Double-click the ZIP file. You will get the file T-Rex.app. 3. Move to Applications (recommended): Drag T-Rex.app into your Applications folder. 4. Start the app: Double-click T-Rex.app. First start: Security warning macOS may show the message: “T-Rex.app cannot be opened because it is from an unidentified developer”. To fix this: Right-click on T-Rex.app Click “Open” Click “Open” again After this, the app will open normally in the future. Running T-Rex on Linux (Ubuntu) 1. Download T-Rex-linux-x86_64.zip. 2. Right-click the ZIP file and select “Extract Here”. 3. Open the extracted folder named “T-Rex-linux-x86_64”. 4. Start the app: Double-click the file named “T-Rex.AppImage”. If nothing happens: Right-click the file and select “Properties” Go to the “Permissions” tab Enable “Allow executing file as program” Try opening the file again If the app still fails to open or shows an error: Install the package libfuse2: sudo apt install libfuse2This package is normally preinstalled on Ubuntu, but in rare cases it may be missing. Running T-Rex on Windows (≥Windows 11) T-Rex runs on Windows using WSL2 (Windows Subsystem for Linux). 1. Install WSL2 Follow Microsoft’s official installation guide: https://learn.microsoft.com/en-us/windows/wsl/install Restart your computer if required. 2. Set up Ubuntu After installing WSL2, install Ubuntu from the Microsoft Store and open it. 3. Download the Linux version of T-Rex Download T-Rex-linux-x86_64.zip. 4. Continue with Linux instructions Once Ubuntu is set up, follow the instructions for “Running T-Rex on Linux (Ubuntu)” to extract and start the application. Test Files T-Rex can be tested by downloading the file “trio-test-data.zip”.The dataset contains FASTQ, BAM, VCF, and TSV files from three artificial trios. The dataset is very small and only requires a few minutes to run. The dataset includes four variants with a gnomAD allele frequency of approximately 85%.To ensure that all variants are displayed in the application, please set the maximum allele frequency to 100%. Source Code & Citation The full source code is available on GitHub. Please cite the software using the Zenodo archive DOI.