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Updated: Feb 21, 2026

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
Published on: March 15, 2019
Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis
Felix Lenner1,2,3, Anders Jemt2,3, Lucia Peña Pérez3,4,5
1Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, 751 08, Sweden.
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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