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 Nallo is available from GitHub: https://github.com/genomic-medicine-sweden/nallo
Lenner et al. (Thu,) studied this question.