{"entity": "publication", "iuid": "dc50be43c77c4c738ce02000e2b3545d", "timestamp": "2026-08-13T20:14:05.164Z", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc50be43c77c4c738ce02000e2b3545d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc50be43c77c4c738ce02000e2b3545d"}}, "title": "Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis.", "authors": [{"family": "Lenner", "given": "Felix", "initials": "F"}, {"family": "Jemt", "given": "Anders", "initials": "A"}, {"family": "Pe\u00f1a P\u00e9rez", "given": "Lucia", "initials": "L"}, {"family": "Neethiraj", "given": "Ramprasad", "initials": "R"}, {"family": "Pruisscher", "given": "Peter", "initials": "P"}, {"family": "Schmitz", "given": "Daniel", "initials": "D"}, {"family": "Renevey", "given": "Annick", "initials": "A"}, {"family": "Corcoran", "given": "P\u00e1draic", "initials": "P"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications.scilifelab.se/researcher/32a701ee07674785b48b047665e18ee6.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A"}, {"family": "Wirta", "given": "Valtteri", "initials": "V"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "journal article", "published": "2026-02-28", "journal": {"title": "Bioinformatics", "issn": "1367-4811", "volume": "42", "issue": "3", "issn-l": "1367-4803"}, "abstract": "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.\n\nHere 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.\n\nNallo is available from GitHub: https://github.com/genomic-medicine-sweden/nallo.", "doi": "10.1093/bioinformatics/btag086", "pmid": "41712762", "labels": {"NGI Long read": "Technology development", "NGI Uppsala (Uppsala Genome Center)": "Technology development", "National Genomics Infrastructure": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC12988770"}, {"db": "pii", "key": "8490763"}], "notes": [], "created": "2026-08-12T15:00:28.150Z", "modified": "2026-08-12T15:00:28.263Z"}