JSON
Lenner F, Jemt A, Peña Pérez L, Neethiraj R, Pruisscher P, Schmitz D, Renevey A, Corcoran P, Nilsson D, Eisfeldt J, Lindstrand A, Wirta V, Ameur A, Feuk L
Bioinformatics 42 (3) - [2026-02-28; online 2026-02-19]
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. 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. Nallo is available from GitHub: https://github.com/genomic-medicine-sweden/nallo.
NGI Long read [Technology development]
NGI Uppsala (Uppsala Genome Center) [Technology development]
National Genomics Infrastructure [Technology development]
PubMed 41712762
DOI 10.1093/bioinformatics/btag086
Crossref 10.1093/bioinformatics/btag086
pmc: PMC12988770
pii: 8490763