RTG Core. The powerful, open-source engine behind our custom genomics solutions.
RTG Core delivers an end-to-end solution for a complete range of applications including variant detection for singletons, families, large pedigrees and populations, cancer, structural variant and CNV analysis, and microbial and metagenomic analysis. It contains all the functionality of our entire range of specialized pipelines in a single package.
While you are free to download and use RTG Core out-of-the-box, its true power lies in its flexibility. We utilize RTG Core as a robust foundation to build and deploy custom, end-to-end bioinformatics solutions tailored to our clients’ unique diagnostic and research needs.
Technical Highlights
Built on over a decade of algorithmic innovation, RTG Core includes advanced features that set it apart:
Pedigree & Sex-Aware Joint Calling: Joint Bayesian calling of multiple samples in pedigrees of varying relatedness. Automatically phases offspring variants from inheritance and handles specific confidence scoring for de novo discovery. Automatically maps to the correct chromosomes based on sample sex.
Somatic Variant Detection: Joint Bayesian somatic variant detection, including support for sample contamination and post-calling updated contamination estimates.
Comprehensive Metagenomic Analysis: Fast pipelines for species frequency composition and abundance analysis, including interactive Krona visualizations and contaminant filtering.
Variant Comparison & Benchmarking: Includes sophisticated variant comparison tools for benchmarking and ROC analysis to guide variant scoring and filtering, including tools for visualization of ROC information between runs.
Strict Reproducibility: Unlike many other tools, RTG Core results do not change when you enable multi-threading or repeat the exact same run.
Supported Applications
RTG Core’s broad capabilities support a wide range of research and medical genomics applications:
Medical Genomic Research & Personalized Medicine: Establish reliable, high-throughput processing pipelines for individual or multiple human genomes. Utilize pedigree information for families or larger cohorts for accurate variant discovery. Compare sequence and structural variation between normal and disease genomes to identify causal loci.
Metagenomics & Microbiome Analysis: Utilize RTG mapping for focused research applications such as metagenomic species identification, community analysis, and metabolic pathway analysis.
Plant & Agricultural Genomics: Investigate new crop species and detect variants in genetically diverse strains. Flexible sensitivity tuning allows you to handle the high error rates associated with unique combinations of genome-specific mutations and aggressive cross-species comparisons.
Why we open-sourced it
Few organisations can justify building and maintaining this depth of genomic analysis capability in-house. Over the years our team of scientists and engineers has developed a comprehensive suite of NGS analysis tools with advanced features available nowhere else, and we are proud to offer it to the community free under the permissive BSD open-source licence.
These products streamline your analysis from raw data to high-quality variants, and serve as the foundation for our Custom Genomic Solutions and Services, demonstrating the computational expertise and robust engineering we bring to your custom pipelines and projects.
Genomics has entered a new era where hospitals, research centers, and companies can no longer afford to develop the assets, technology, and talent within their own organization required to stay ahead. Over the years, our world-class team of scientists and engineers has developed a comprehensive suite of tools for NGS analysis containing advanced features available nowhere else.
We are proud to offer our world-class bioinformatics software to the community for free under the permissive BSD open-source license.
These products not only streamline your analysis from raw data to high-quality results, but also serve as the foundation for our Custom Genomic Solutions and Services, demonstrating the deep computational expertise and robust engineering we can bring to your custom pipelines and projects.
Source Code & Downloads
Documentation
Need help integrating RTG Core into your workflow? We offer professional Custom Genomic Solutions and Services including pipeline integration, web portal development, and proprietary algorithm design. Contact us to discuss your project.