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

<h4>Motivation</h4>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.<h4>Results</h4>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.<h4>Availability and implementation</h4>Nallo is available from GitHub: https://github.com/genomic-medicine-sweden/nallo.