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:

1. Reference data (biological datasets)
2. 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).