ArticleBioinformatics (Oxford, England)2026
Taming the reference genome jungle: the refget sequence collection standard.
Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Model Context Protocol: The unexpected catalyst of a bioinformatics interoperability revolution.PLoS computational biology · 2026Article
- GBZ-base and GAF-base: Indexed pangenome file formats.bioRxiv : the preprint server for biology · 2026Article
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationReference genomes are foundational to genomics but suffer from widespread ambiguity and incompatibility due to inconsistent naming, undocumented differences, and lack of formal mechanisms for comparison.
resultsTo address this, we introduce the GA4GH refget Sequence Collections (seqcol) standard. Refget seqcol is a framework for unambiguous representation, retrieval, and comparison of sequence collections such as reference genomes and transcriptomes. The seqcol standard comprises four components: a structured data schema, a canonical encoding algorithm that produces content-based, globally unique identifiers, a retrieval API, and a comparison protocol. This standard enables precise identification of sequence collections, even across decentralized or private systems, and allows compatibility assessments beyond exact identity, such as order-relaxed matches or shared coordinate systems. We applied the refget seqcol standard to 60 human and 36 mouse reference genomes sourced from major providers. Using digest-based comparisons, we quantified levels of similarity across attributes including sequence names, lengths, coordinate systems, and actual sequence content. Our analysis revealed some consistent subsets of sequences or coordinate systems, as well as substantial incompatibility among references and duplicate references under different names. This work offers a scalable, reproducible solution to the reference genome compatibility crisis, enabling improved transparency, reuse, and integration in genomic analyses. Refget seqcol enhances interoperability across tools and datasets, making genomic research more robust and reproducible. AVAILABILITY AND IMPLEMENTATION: To support adoption of refget seqcol, we provide a Python package implementing the full standard, a web API, and a comparison interface allowing users to assess local references against a curated database. The formal specification is hosted at https://ga4gh.github.io/refget/ and the reference implementation can be found at https://github.com/refgenie/refget.
Identifiers
42535916What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.