UMI-nea: a fast, robust tool for reference-free UMI deduplication and accurate quantification.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40973030", "kind": "science-record", "revision": 3, "content_hash": "sha256:eca73295488bb7417643a01889fb8b41b62b28998917f00dd30d2846cb13cb81", "created_at": "2026-11-01T20:31:03Z", "updated_at": "2026-11-01T22:14:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "UMI-nea: a fast, robust tool for reference-free UMI deduplication and accurate quantification.", "doi": "10.1093/bioinformatics/btaf514", "pmid": "40973030", "authors": ["Jixin Deng", "Jingxiao Zhang", "Song Tian", "John DiCarlo", "Hong Xu", "Samuel J Rulli", "Jonathan M Shaffer", "Vikas Gupta", "Toeresin Karakoyun"], "journal": "Bioinformatics (Oxford, England)", "year": 2025, "abstract": "MOTIVATION: One of the key applications of Unique Molecular Identifiers (UMIs) in high-throughput sequencing is to correct for PCR amplification bias and removal of PCR duplicates, thereby improving quantification in DNA-seq and RNA-seq applications. Accurately grouping error-bearing UMIs that originate from the same input molecule through a UMI deduplication method is a critical step in this process. However, many existing UMI deduplication tools rely on simple Hamming distance comparisons or suboptimal clustering algorithms, often resulting in erroneous UMI groupings, particularly in error-prone long-read sequencing or ultra-high-depth short-read sequencing.\nRESULTS: We introduce UMI-nea, a tool that utilizes Levenshtein distance comparisons and a novel clustering approach to optimize multithreading workflows. Compared against three other indel-aware UMI deduplication tools, UMI-nea achieves more accurate UMI groupings with efficient run time. It demonstrates robust performance across diverse sequencing platforms, depths, and UMI lengths. Additionally, UMI-nea incorporates a data-guided adaptive UMI filter, further enhancing quantification accuracy.\nAVAILABILITY AND IMPLEMENTATION: UMI-nea is available on github https://github.com/Qiaseq-research/UMI-nea.git or Zenodo https://doi.org/10.5281/zenodo.16745758. Sequencing data are stored at https://qiagenpublic.blob.core.windows.net/umi-nea-datasets/.", "claims": [{"id": "claim-method", "statement": "using the V-measure (Rosenberg and Hirschberg 2007) to assess clustering accuracy", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40973030", "locator": "sections[2] \"2 Methods\" paragraph 6", "quote": "using the V-measure (Rosenberg and Hirschberg 2007) to assess clustering accuracy"}], "state": "complete"}, {"id": "claim-data-access", "statement": "Sequencing data are stored at https://qiagenpublic.blob.core.windows.net/umi-nea-datasets/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40973030", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Sequencing data are stored at https://qiagenpublic.blob.core.windows.net/umi-nea-datasets/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "UMI-nea achieved the highest V-measure and produced UMI cluster counts closest to the true founder numbers in most datasets, while exhibiting the lowest variability in both metrics.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40973030", "locator": "sections[4] \"3.1 UMI deduplication performance comparison\" paragraph 6", "quote": "While UMI-nea achieves the highest V-measure and produces UMI cluster counts closest to the true founder numbers in most datasets, it also exhibits the lowest variability in both metrics."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "UMI-nea achieved the highest V-measure and produced UMI cluster counts closest to the true founder numbers in most datasets, while exhibiting the lowest variability in both metrics.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40973030"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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