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Identity and compatibility of reference genome resources
Michał Stolarczyk1, Bingjie Xue1, Nathan C Sheffield1
1Center for Public Health Genomics, University of Virginia, Virginia, 22908, USA.
NAR Genomics and Bioinformatics
|May 21, 2021
Summary
We developed a new method to track reference genome data, ensuring compatibility and reproducibility in genomic analysis. This approach uses unique identifiers and relationships to manage diverse genome resources effectively.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Genome analysis requires diverse reference data (sequences, annotations, indexes) from multiple sources and versions.
- Identifying and assessing compatibility among these reference data is a significant challenge in bioinformatics.
- Lack of standardized methods hinders data portability, reproducibility, and re-use in genomic studies.
Purpose of the Study:
- To introduce a novel approach for establishing the identity and compatibility of reference genome resources.
- To address the challenges of managing and verifying diverse genome data versions and sources.
- To enhance the portability, reproducibility, and re-use of critical genome reference data.
Main Methods:
- Derivation of unique identifiers for each individual reference genome resource.
- Recording parent-child relationships to establish lineage and provenance among resources.
- Implementation of recursive identifiers to determine resource identity and coordinate system compatibility.
Main Results:
- A system for uniquely identifying and tracking reference genome data.
- Established methods for assessing compatibility between different genome resources, including coordinate systems.
- Facilitated improved data management for genomic analysis workflows.
Conclusions:
- The developed approach enhances the reliability and usability of reference genome data.
- This method supports greater reproducibility and portability in genomic research.
- The system promotes efficient re-use of genome reference data across various analyses.
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