{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T03:36:42Z","timestamp":1769830602987,"version":"3.49.0"},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,12,30]],"date-time":"2025-12-30T00:00:00Z","timestamp":1767052800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T00:00:00Z","timestamp":1769731200000},"content-version":"vor","delay-in-days":31,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Swiss Federal Institute of Technology Zurich"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Pangenome graphs integrate multiple assemblies to represent non-redundant genetic diversity. However, current evaluations of pangenome graphs rely primarily on technical parameters (e.g., total length, number of nodes\/edges, growth curves), which fail to assess how effectively the graph represents homologous stretches across the integrated assemblies and how well short reads align against pangenome graph references.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce a novel method to quantitatively assess how well a pangenome graph represents its integrated assemblies. Our method quantifies how many single-copy and universal k-mers from the source assemblies are uniquely and completely represented within the graph nodes. Implemented in the open-source tool PG-SCUnK, this approach identifies the fractions of unique, duplicated, and split k-mers, which correlate with short read mapping rates to the pangenome graph.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Insights provided by PG-SCUnK facilitate the selection of appropriate parameters to build optimal reference pangenome graphs.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-025-06355-2","type":"journal-article","created":{"date-parts":[[2025,12,30]],"date-time":"2025-12-30T14:14:53Z","timestamp":1767104093000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers"],"prefix":"10.1186","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0276-7462","authenticated-orcid":false,"given":"Tristan","family":"Cumer","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0009-0006-9409-1987","authenticated-orcid":false,"given":"Sotiria","family":"Milia","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8425-5630","authenticated-orcid":false,"given":"Alexander S.","family":"Leonard","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0501-6760","authenticated-orcid":false,"given":"Hubert","family":"Pausch","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,12,30]]},"reference":[{"key":"6355_CR1","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1038\/s41586-020-2371-0","volume":"583","author":"HJ Abel","year":"2020","unstructured":"Abel HJ, Larson DE, Regier AA, et al. Mapping and characterization of structural variation in 17,795 human genomes. Nature. 2020;583:83\u20139.","journal-title":"Nature"},{"key":"6355_CR2","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1038\/nature15393","volume":"526","author":"A Auton","year":"2015","unstructured":"Auton A, Abecasis GR, Altshuler DM, et al. A global reference for human genetic variation. Nature. 2015;526:68\u201374.","journal-title":"Nature"},{"key":"6355_CR3","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2409943121","volume":"121","author":"B Fang","year":"2024","unstructured":"Fang B, Edwards SV. Fitness consequences of structural variation inferred from a House Finch pangenome. Proc Natl Acad Sci U S A. 2024;121:e2409943121.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"6355_CR4","doi-asserted-by":"publisher","unstructured":"Garrison E, Guarracino A, Heumos S et al. 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