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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.
Nallo is a new Nextflow pipeline designed for comprehensive long-read sequencing data analysis. It supports PacBio and Oxford Nanopore technologies, aiding rare disease research by detecting genetic variants and performing genome assembly.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Long-read sequencing (LRS) is crucial for human medical research and diagnostics, offering complete genome information.
- A need exists for robust, user-friendly pipelines for comprehensive LRS data analysis.
Purpose of the Study:
- To introduce Nallo, a Nextflow pipeline for analyzing long-read sequencing data.
Main Methods:
- Nallo processes PacBio and Oxford Nanopore sequencing data.
- The pipeline integrates variant detection, genome assembly, and CpG methylation analysis.
- It includes annotation and functional consequence ranking for genetic variants.
Main Results:
- Nallo provides a comprehensive analysis of LRS data.
- It supports rare disease research projects.
- The pipeline facilitates variant interpretation through annotation and ranking.
Conclusions:
- Nallo offers a robust and accessible solution for long-read sequencing data analysis.
- It enhances the utility of LRS in medical research and diagnostics, particularly for rare diseases.
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