Evidence map›Paper›PMID 41712762›Full record

ArticleBioinformatics (Oxford, England)2026

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

Felix Lenner, Anders Jemt, Lucia Peña Pérez, Ramprasad Neethiraj, Peter Pruisscher, Daniel Schmitz, Annick Renevey, Pádraic Corcoran, Daniel Nilsson, Jesper Eisfeldt and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Felix LennerDepartment of Immunology, Genetics and Pathology, Uppsala University, Uppsala, 751 08, Sweden.
Anders JemtGenomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, 171 77, Sweden.
Lucia Peña PérezScience for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden.
Ramprasad NeethirajScience for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden.
Peter PruisscherScience for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden.
Daniel SchmitzClinical Genomics Gothenburg, SciLifeLab, Sahlgrenska Academy, University of Gothenburg, Göteborg, 405 30, Sweden.
Annick ReneveyScience for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden.
Pádraic CorcoranDepartment of Immunology, Genetics and Pathology, Uppsala University, Uppsala, 751 08, Sweden.
Daniel NilssonScience for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden.
Jesper EisfeldtDepartment of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, 171 77, Sweden.ORCID 0000-0003-3716-4917
Anna LindstrandDepartment of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, 171 77, Sweden.
Valtteri WirtaGenomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, 171 77, Sweden.
Adam AmeurDepartment of Immunology, Genetics and Pathology, Uppsala University, Uppsala, 751 08, Sweden.ORCID 0000-0001-6085-6749
Lars FeukDepartment of Immunology, Genetics and Pathology, Uppsala University, Uppsala, 751 08, Sweden.ORCID 0000-0003-2355-2919

Funding

Genomic Medicine Sweden and funding from Hjärnfonden FO2022-0207
6 · The paper itself

Abstract

motivationLong-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.

resultsHere 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.

Indexed as

Genome, HumanGenomicsHigh-Throughput Nucleotide SequencingSequence Analysis, DNASoftwareDNA MethylationHumans

Identifiers

PMID41712762
PMCPMC12988770

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.