T-Rex Reference Data and Binaries

Description This dataset contains processed reference files and precompiled software binaries for use with the T-Rex (Trio Rare Variant Analysis of Exomes) application. The files are derived from publicly available resources and have been preprocessed to ensure compatibility with the T-Rex analysis pipeline. The software binaries include all required third-party executables used by the T-Rex pipeline. These are provided to ensure reproducibility and simplify installation, and are separated by operating system. The release consists of two types of components: Reference data (biological datasets) Precompiled software binaries required to run the T-Rex pipeline Both components are distributed as pre-packaged archives: trex_ref_data.zip – processed reference datasets apps_macos.zip – macOS-specific binaries apps_linux.zip – Linux-specific binaries Each archive must be downloaded and extracted into the corresponding folders of the T-Rex installation directory: ref_data.zip → ./ref_data/ apps_macos.zip → ./apps/ (macOS users only) apps_linux.zip → ./apps/ (Linux users only) Source Datasets Original sources: - Homo sapiens reference genome GRCh38 (Ensembl) - Source: https://ftp.ensembl.org/pub/release-113/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz - © EMBL-EBI and the Ensembl project - License: Creative Commons Attribution 4.0 International (CC BY 4.0) - Genome Aggregation Database (gnomAD) v4.0 - Source: https://gnomad.broadinstitute.org - © Broad Institute - License: Creative Commons Attribution 4.0 International (CC BY 4.0) - ClinVar variant database - Source: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Provided by the National Center for Biotechnology Information (NCBI) - License: Public Domain (U.S. Government Work) Modifications The original datasets were modified to ensure compatibility with the T-Rex pipeline.These modifications include: - File format standardization - Subsetting and filtering of relevant data - Indexing and preprocessing for efficient analysis No changes were made to the biological interpretation of the data. Notes - This distribution includes both reference data and required software binaries.- It is intended for research use only.- The original datasets and binaries remain available from their respective sources. - Users may alternatively download and preprocess the original data manually. - All third-party tools are executed as separate programs via command-line calls. They are included as unmodified binaries or JAR files.- Each tool remains under its own license. A complete and detailed list of components, licenses, and source references is provided in LICENSES.txt. T-Rex invokes these tools as independent executables. No modifications have been made unless explicitly stated.- If you use this dataset, please cite both the original sources of the reference data and binaries as specified in LICENSES.txt and the T-Rex application paper as indicated on GitHub. Related Software The T-Rex application is available separately and distributed under the GNU General Public License v3.0 (GPLv3).