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TREX is a Tandem Repeat Expansion Analysis Pipeline. This pipeline provides an end-to-end, reproducible framework for the genome-wide analysis of tandem repeat (TR) expansions from whole-genome sequencing data. |
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TREX is a Tandem Repeat Expansion Analysis Pipeline. This pipeline provides an end-to-end, reproducible framework for the genome-wide analysis of tandem repeat (TR) expansions from whole-genome sequencing data. It enables systematic detection, characterization, and biological interpretation of repeat expansions across multiple cohorts and phenotypic groups, with an emphasis on statistical rigor and downstream functional relevance.
- Genome-wide TR expansion analysis across single or multiple cohorts
- Cohort-aware modeling, supporting case–control and multi-group study designs
- Robust statistical framework integrating burden tests, non-parametric comparisons, and regression modeling
- Biological contextualization of expansions via genomic annotation, regulatory proximity, and gene set enrichment
- Flexible filtering strategies, including private vs shared expansions and pure vs mixed group assignments
- Integrated functional enrichment and network analysis, with optional Cytoscape visualization
- Fully reproducible execution, implemented as a modular Snakemake workflow with YAML-based configuration
Full documentation is available in the Documents directory, including:
Clone repository
git lfs install
git clone https://github.com/RacheleRR/TREX.git
cd TREX
Run setup
bash setup/setup.sh
Dry run
snakemake -n
Run pipeline
snakemake --cores 12
If you use this pipeline, please cite:
- ExpansionHunterDenovo: Dolzhenko et al. (2020) Genome Biology
- g:Profiler: Raudvere et al. (2019) Nucleic Acids Research
- DBSCAN: Ester et al. (1996) KDD-96
- Fazal et al. (2020) - EHDN helper scripts
- Trost et al. (2020) - BTlib utilities
MIT License - see LICENSE file
For questions or issues, please open a GitHub issue or contact [your email].