{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T02:54:18Z","timestamp":1775876058996,"version":"3.50.1"},"reference-count":64,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2021,11,2]],"date-time":"2021-11-02T00:00:00Z","timestamp":1635811200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002347","name":"Federal Ministry of Education and Research","doi-asserted-by":"crossref","award":["FKZ 031L0180"],"award-info":[{"award-number":["FKZ 031L0180"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"crossref"}]},{"name":"German Research Foundation (DFG) through subproject A6","award":["CRC 1404"],"award-info":[{"award-number":["CRC 1404"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>With the increasing throughput of sequencing technologies, structural variant (SV) detection has become possible across tens of thousands of genomes. Non-reference sequence (NRS) variants have drawn less attention compared with other types of SVs due to the computational complexity of detecting them. When using short-read data, the detection of NRS variants inevitably involves a de novo assembly which requires high-quality sequence data at high coverage. Previous studies have demonstrated how sequence data of multiple genomes can be combined for the reliable detection of NRS variants. However, the algorithms proposed in these studies have limited scalability to larger sets of genomes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce PopIns2, a tool to discover and characterize NRS variants in many genomes, which scales to considerably larger numbers of genomes than its predecessor PopIns. In this article, we briefly outline the PopIns2 workflow and highlight our novel algorithmic contributions. We developed an entirely new approach for merging contig assemblies of unaligned reads from many genomes into a single set of NRS using a colored de Bruijn graph. Our tests on simulated data indicate that the new merging algorithm ranks among the best approaches in terms of quality and reliability and that PopIns2 shows the best precision for a growing number of genomes processed. Results on the Polaris Diversity Cohort and a set of 1000 Icelandic human genomes demonstrate unmatched scalability for the application on population-scale datasets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The source code of PopIns2 is available from https:\/\/github.com\/kehrlab\/PopIns2.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab749","type":"journal-article","created":{"date-parts":[[2021,10,28]],"date-time":"2021-10-28T15:14:33Z","timestamp":1635434073000},"page":"604-611","source":"Crossref","is-referenced-by-count":16,"title":["Population-scale detection of non-reference sequence variants using colored de Bruijn graphs"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5525-1849","authenticated-orcid":false,"given":"Thomas","family":"Krannich","sequence":"first","affiliation":[{"name":"Berlin Institute of Health at Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin , Charit\u00e9platz 1, 10117 Berlin, Germany"}]},{"given":"W Timothy J","family":"White","sequence":"additional","affiliation":[{"name":"Google Inc. , 8002 Z\u00fcrich, Switzerland"}]},{"given":"Sebastian","family":"Niehus","sequence":"additional","affiliation":[{"name":"Regensburg Center for Interventional Immunology (RCI), 93053 Regensburg, Germany"}]},{"given":"Guillaume","family":"Holley","sequence":"additional","affiliation":[{"name":"deCODE Genetics, Reykjav\u00edk 102, Iceland"}]},{"given":"Bjarni V","family":"Halld\u00f3rsson","sequence":"additional","affiliation":[{"name":"deCODE Genetics, Reykjav\u00edk 102, Iceland"},{"name":"Department of Engineering, School of Technology, Reykjav\u00edk University, Reykjav\u00edk 102, Iceland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3417-7504","authenticated-orcid":false,"given":"Birte","family":"Kehr","sequence":"additional","affiliation":[{"name":"Berlin Institute of Health at Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin , Charit\u00e9platz 1, 10117 Berlin, Germany"},{"name":"Regensburg Center for Interventional Immunology (RCI), 93053 Regensburg, Germany"},{"name":"Universit\u00e4t Regensburg, 93053 Regensburg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2021,11,2]]},"reference":[{"key":"2023020108503480300_btab749-B1","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/s41586-020-2371-0","article-title":"Mapping and characterization of structural variation in 17,795 human genomes","volume":"583","author":"Abel","year":"2020","journal-title":"Nature"},{"key":"2023020108503480300_btab749-B2","doi-asserted-by":"crossref","DOI":"10.1016\/j.csbj.2021.06.047","article-title":"Buffering updates enables efficient dynamic de Bruijn Graphs","author":"Alanko","year":"2021","journal-title":"Comput. 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