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

Felix Lenner; Anders Jemt; Lucia Pe&#xf1;a P&#xe9;rez; Ramprasad Neethiraj; Peter Pruisscher; Daniel Schmitz; Annick Renevey; P&#xe1;draic Corcoran; Daniel Nilsson; Jesper Eisfeldt; Anna Lindstrand; Valtteri Wirta; Adam Ameur; Lars Feuk

doi:10.1093/bioinformatics/btag086

PubMed · 41712762

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

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·Adam Ameur·Lars Feuk

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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.

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Humans Genome, Human Software Genomics High-Throughput Nucleotide Sequencing Sequence Analysis, DNA DNA Methylation Journal Article Research Support, Non-U.S. Gov't

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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, Adam Ameur, Lars Feuk. 2026-02-28. Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis.. https://doi.org/10.1093/bioinformatics%2Fbtag086

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