{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T20:21:27Z","timestamp":1773519687561,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T00:00:00Z","timestamp":1771459200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Genomic Medicine Sweden and funding from Hj\u00e4rnfonden","award":["FO2022-0207"],"award-info":[{"award-number":["FO2022-0207"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,2,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Long-read sequencing (LRS) is increasingly used for human medical research and clinical diagnostics due to its capacity to generate complete genome information. However, there is a lack of robust and easy-to-use pipelines for comprehensive LRS data analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here we present Nallo, a Nextflow pipeline for analysis of PacBio and Oxford Nanopore data, with additional support for rare disease research projects. The pipeline detects a wide range of genetic variants, performs genome assembly, and reports CpG methylation. It also enables annotation and ranking of variants based on their predicted functional consequences.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Nallo is available from GitHub: https:\/\/github.com\/genomic-medicine-sweden\/nallo<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag086","type":"journal-article","created":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T12:54:30Z","timestamp":1771505670000},"source":"Crossref","is-referenced-by-count":1,"title":["Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis"],"prefix":"10.1093","volume":"42","author":[{"given":"Felix","family":"Lenner","sequence":"first","affiliation":[{"name":"Department of Immunology, Genetics and Pathology, Uppsala University , Uppsala, 751 08,","place":["Sweden"]},{"name":"Genomic Medicine Center Karolinska, Karolinska University Hospital , Stockholm, 171 77,","place":["Sweden"]},{"name":"Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm, 171 77,","place":["Sweden"]}]},{"given":"Anders","family":"Jemt","sequence":"additional","affiliation":[{"name":"Genomic Medicine Center Karolinska, Karolinska University Hospital , Stockholm, 171 77,","place":["Sweden"]},{"name":"Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm, 171 77,","place":["Sweden"]}]},{"given":"Lucia","family":"Pe\u00f1a P\u00e9rez","sequence":"additional","affiliation":[{"name":"Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm, 171 77,","place":["Sweden"]},{"name":"Centre for Inherited Metabolic Diseases, Karolinska University Hospital , Stockholm, 171 77,","place":["Sweden"]},{"name":"Department of Molecular Medicine and Surgery, Karolinska Institutet , Stockholm, 171 77,","place":["Sweden"]}]},{"given":"Ramprasad","family":"Neethiraj","sequence":"additional","affiliation":[{"name":"Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm, 171 77,","place":["Sweden"]}]},{"given":"Peter","family":"Pruisscher","sequence":"additional","affiliation":[{"name":"Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm, 171 77,","place":["Sweden"]}]},{"given":"Daniel","family":"Schmitz","sequence":"additional","affiliation":[{"name":"Clinical Genomics Gothenburg, SciLifeLab, Sahlgrenska Academy, University of Gothenburg , G\u00f6teborg, 405 30,","place":["Sweden"]}]},{"given":"Annick","family":"Renevey","sequence":"additional","affiliation":[{"name":"Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm, 171 77,","place":["Sweden"]}]},{"given":"P\u00e1draic","family":"Corcoran","sequence":"additional","affiliation":[{"name":"Department of Immunology, Genetics and Pathology, Uppsala University , Uppsala, 751 08,","place":["Sweden"]},{"name":"SciLifeLab, Uppsala University , Uppsala, 751 08,","place":["Sweden"]}]},{"given":"Daniel","family":"Nilsson","sequence":"additional","affiliation":[{"name":"Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm, 171 77,","place":["Sweden"]},{"name":"Department of Clinical Genetics and Genomics, Karolinska University Hospital , Stockholm, 171 77,","place":["Sweden"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3716-4917","authenticated-orcid":false,"given":"Jesper","family":"Eisfeldt","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine and Surgery, Karolinska Institutet , Stockholm, 171 77,","place":["Sweden"]},{"name":"Department of Clinical Genetics and Genomics, Karolinska University Hospital , Stockholm, 171 77,","place":["Sweden"]}]},{"given":"Anna","family":"Lindstrand","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine and Surgery, Karolinska Institutet , Stockholm, 171 77,","place":["Sweden"]},{"name":"Department of Clinical Genetics and Genomics, Karolinska University Hospital , Stockholm, 171 77,","place":["Sweden"]}]},{"given":"Valtteri","family":"Wirta","sequence":"additional","affiliation":[{"name":"Genomic Medicine Center Karolinska, Karolinska University Hospital , Stockholm, 171 77,","place":["Sweden"]},{"name":"Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm, 171 77,","place":["Sweden"]},{"name":"Department of Clinical Genetics and Genomics, Karolinska University Hospital , Stockholm, 171 77,","place":["Sweden"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6085-6749","authenticated-orcid":false,"given":"Adam","family":"Ameur","sequence":"additional","affiliation":[{"name":"Department of Immunology, Genetics and Pathology, Uppsala University , Uppsala, 751 08,","place":["Sweden"]},{"name":"SciLifeLab, Uppsala University , Uppsala, 751 08,","place":["Sweden"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2355-2919","authenticated-orcid":false,"given":"Lars","family":"Feuk","sequence":"additional","affiliation":[{"name":"Department of Immunology, Genetics and Pathology, Uppsala University , Uppsala, 751 08,","place":["Sweden"]},{"name":"SciLifeLab, Uppsala University , Uppsala, 751 08,","place":["Sweden"]}]}],"member":"286","published-online":{"date-parts":[[2026,2,19]]},"reference":[{"key":"2026031412410986100_btag086-B1","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di Tommaso","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2026031412410986100_btag086-B2","doi-asserted-by":"crossref","DOI":"10.1126\/science.abf7117","article-title":"Haplotype-resolved diverse human genomes and integrated analysis of structural variation","volume":"372","author":"Ebert","year":"2021","journal-title":"Science"},{"key":"2026031412410986100_btag086-B3","doi-asserted-by":"crossref","first-page":"1774","DOI":"10.1101\/gr.279510.124","article-title":"A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities","volume":"34","author":"Eisfeldt","year":"2024","journal-title":"Genome Res"},{"key":"2026031412410986100_btag086-B4","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The nf-core framework for community-curated bioinformatics pipelines","volume":"38","author":"Ewels","year":"2020","journal-title":"Nat 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reference genomes","volume":"611","author":"Jarvis","year":"2022","journal-title":"Nature"},{"key":"2026031412410986100_btag086-B9","volume-title":"Genome Biol.","author":"Langer","year":"2025"},{"key":"2026031412410986100_btag086-B10","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1038\/s41467-024-44804-3","article-title":"Utility of long-read sequencing for all of us","volume":"15","author":"Mahmoud","year":"2024","journal-title":"Nat Commun"},{"key":"2026031412410986100_btag086-B11","article-title":"Unravelling undiagnosed rare disease cases by HiFi long-read genome sequencing","volume":"35","author":"Steyaert","journal-title":"Genome Res"},{"key":"2026031412410986100_btag086-B12","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s13073-021-00855-5","article-title":"Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients","volume":"13","author":"Stranneheim","year":"2021","journal-title":"Genome Med"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag086\/66993640\/btag086.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/3\/btag086\/66993640\/btag086.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/3\/btag086\/66993640\/btag086.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T16:41:22Z","timestamp":1773506482000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag086\/8490763"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2026,2,19]]},"references-count":12,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,2,28]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag086","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,3]]},"published":{"date-parts":[[2026,2,19]]},"article-number":"btag086"}}