Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis

Bioinformatics 2026 Open access

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Authors: Felix Lenner, Anders Jemt, Lucia Peña Pérez, Ramprasad Neethiraj, Peter Pruisscher, Daniel Schmitz, Annick Renevey, Pádraic Corcoran, Daniel Nilsson, Jesper Eisfeldt, Anna Lindstrand, Valtteri Wirta
+2 more Adam Ameur, Lars Feuk
DOI: 10.1093/bioinformatics/btag086
Cited by: 2
References: 9

Abstract

MOTIVATION: 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. RESULTS: 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. AVAILABILITY AND IMPLEMENTATION: Nallo is available from GitHub: https://github.com/genomic-medicine-sweden/nallo.

Fields of Study & Subjects

Genomics and Rare Diseases Genomics and Phylogenetic Studies Cancer Genomics and Diagnostics

Publication details

Journal / source
Bioinformatics
Publisher
Oxford University Press (OUP)
Volume
42
Issue
3
Publication date
19 February 2026
Language
EN