{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T18:35:19Z","timestamp":1789065319043,"version":"build-2803163510"},"reference-count":19,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T00:00:00Z","timestamp":1743033600000},"content-version":"vor","delay-in-days":26,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Current Protocols"],"published-print":{"date-parts":[[2025,3]]},"abstract":"Abstract<\/jats:title>Long\u2010read sequencing platforms such as the Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) platforms now offer sufficient read lengths, throughput, and accuracy at competitive costs to analyze polymorphic regions of the human genome, including the highly complex human leukocyte antigen (HLA) gene\u00a0cluster\u2014a cornerstone of human immunity. Here, we present a streamlined protocol for predicting HLA signatures from whole\u2010genome shotgun (WGS) long\u2010read sequencing data by directly streaming sequence alignments into HLAminer. This method is as simple as running minimap2, scales efficiently with the number of sequences, and works with any read aligner compatible with the SAM file format\u2014eliminating the need to store bulky alignment files on disk. We provide a step\u2010by\u2010step guide for predicting HLA class I and class II alleles from third\u2010generation long\u2010read sequencing data and demonstrate the robustness of predictions even with older, less accurate WGS nanopore datasets and relatively low (10\u00d7) sequencing coverage. Code availability: HLAminer is available under the BC Cancer software license agreement (academic use) at https:\/\/github.com\/bcgsc\/HLAminer<\/jats:ext-link>. \u00a9 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC.<\/jats:p>This article was corrected on 25 April 2025. See the end of the full text for details.<\/jats:p>Basic Protocol<\/jats:bold>: HLA prediction from streamed ONT or PacBio long\u2010read alignments<\/jats:p>","DOI":"10.1002\/cpz1.70124","type":"journal-article","created":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T12:46:49Z","timestamp":1743079609000},"source":"Crossref","is-referenced-by-count":1,"title":["Streaming Long\u2010Read Sequence Alignments for HLA Predictions Using HLAminer"],"prefix":"10.1002","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9890-2293","authenticated-orcid":false,"given":"Ren\u00e9 L.","family":"Warren","sequence":"first","affiliation":[{"name":"BC Cancer Genome Sciences Centre Vancouver BC Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0950-7839","authenticated-orcid":false,"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[{"name":"BC Cancer Genome Sciences Centre Vancouver BC Canada"},{"name":"Department of Medical Genetics University of British Columbia Columbia BC Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2025,3,27]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.77898"},{"issue":"1","key":"e_1_2_6_3_1","first-page":"1","article-title":"Third\u2010generation sequencing: The spearhead towards the radical transformation of modern genomics","volume":"12","author":"Athanasopoulou K.","year":"2022","journal-title":"Life"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac1011"},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010020\u201018564\u20109"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/nri.2017.143"},{"key":"e_1_2_6_7_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005151"},{"key":"e_1_2_6_8_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102164\u201012\u201042"},{"key":"e_1_2_6_9_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059\u2010018\u20101388\u20102"},{"key":"e_1_2_6_10_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"e_1_2_6_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.humimm.2020.04.009"},{"key":"e_1_2_6_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010024\u201044804\u20103"},{"key":"e_1_2_6_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq998"},{"key":"e_1_2_6_14_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu548"},{"key":"e_1_2_6_15_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev\u2010genom\u2010021623\u2010081639"},{"key":"e_1_2_6_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/gpbjnl\/qzaf001"},{"key":"e_1_2_6_17_1","doi-asserted-by":"publisher","DOI":"10.1111\/tan.15355"},{"key":"e_1_2_6_18_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.12368"},{"key":"e_1_2_6_19_1","doi-asserted-by":"publisher","DOI":"10.1186\/gm396"},{"key":"e_1_2_6_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0217-9"}],"container-title":["Current Protocols"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/currentprotocols.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cpz1.70124","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,2]],"date-time":"2025-05-02T13:09:02Z","timestamp":1746191342000},"score":1,"resource":{"primary":{"URL":"https:\/\/currentprotocols.onlinelibrary.wiley.com\/doi\/10.1002\/cpz1.70124"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,3]]},"references-count":19,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2025,3]]}},"alternative-id":["10.1002\/cpz1.70124"],"URL":"https:\/\/doi.org\/10.1002\/cpz1.70124","archive":["Portico"],"relation":{},"ISSN":["2691-1299","2691-1299"],"issn-type":[{"value":"2691-1299","type":"print"},{"value":"2691-1299","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,3]]},"article-number":"e70124"}}