ArticleNAR genomics and bioinformatics2021
Identity and compatibility of reference genome resources.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed.
- Taming the reference genome jungle: the refget sequence collection standard.Bioinformatics (Oxford, England) · 2026Article
- ESR1 mutations and CDK4/6 inhibitor choice shape clonal selection and adaptive cell states during acquired resistance.Genome medicine · 2026Article
- Taming the reference genome jungle: the refget sequence collection standard.bioRxiv : the preprint server for biology · 2025Article
- The molecular basis of lamin-specific chromatin interactions.Nature structural & molecular biology · 2025Article
- CHOIR improves significance-based detection of cell types and states from single-cell data.Nature genetics · 2025Article
- Fine-tuning GBS data with comparison of reference and mock genome approaches for advancing genomic selection in less studied farmed species.BMC genomics · 2025Article
- Opportunities and challenges in sharing and reusing genomic interval data.Frontiers in genetics · 2023Article
- From biomedical cloud platforms to microservices: next steps in FAIR data and analysis.Scientific data · 2022Article
- Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects.GigaScience · 2021Article
- PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments.NAR genomics and bioinformatics · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Genome analysis relies on reference data like sequences, feature annotations, and aligner indexes. These data can be found in many versions from many sources, making it challenging to identify and assess compatibility among them. For example, how can you determine which indexes are derived from identical raw sequence files, or which annotations share a compatible coordinate system? Here, we describe a novel approach to establish identity and compatibility of reference genome resources. We approach this with three advances: first, we derive unique identifiers for each resource; second, we record parent-child relationships among resources; and third, we describe recursive identifiers that determine identity as well as compatibility of coordinate systems and sequence names. These advances facilitate portability, reproducibility, and re-use of genome reference data.
Identifiers
What 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.