ECHO: a nanopore sequencing-based workflow for (epi)genetic profiling of the human repeatome

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Publication Details

Journal
Bioinformatics
Published
2026-09-01
DOI
https://doi.org/10.1093/bioinformatics/btag648
Primary Topic
Genetic Neurodegenerative Diseases
Type
article
Field-Weighted Citation Impact
0.00

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article

ECHO: a nanopore sequencing-based workflow for (epi)genetic profiling of the human repeatome

Leena Putzeys, Athina Vidaki, Brando Poggiali, Jeppe Dyrberg Andersen
Bioinformatics
Genetic Neurodegenerative Diseases
article

ECHO: a nanopore sequencing-based workflow for (epi)genetic profiling of the human repeatome

Leena Putzeys, Athina Vidaki, Brando Poggiali, Jeppe Dyrberg Andersen
article en

Abstract

SUMMARY: The human genome is dominated by repetitive DNA, whose genetic and epigenetic variation plays a key role in gene regulation, genome stability, and disease. Recent advances in long-read sequencing now enable large-scale, haplotype-resolved, and DNA methylation-informative analysis of the human genome, including on previously inaccessible complex and repetitive regions. However, the comprehensive, simultaneous characterisation of the "human repeatome" remains challenging, largely due to the lack of comprehensive tools integrated in a single pipeline that can capture the full spectrum of variation across diverse types of DNA repeats. Here, we present ECHO, a user-friendly, Snakemake-based pipeline for the "(Epi)genomic Characterisation of Human Repetitive Elements using Oxford Nanopore Sequencing". ECHO provides a reproducible and scalable framework for end-to-end analysis of whole-genome nanopore sequencing data, enabling integrative but also tailored (epi)genetic analyses of the human repeatome. AVAILABILITY AND IMPLEMENTATION: ECHO is freely available at Github: https://github.com/leenput/ECHO-pipeline, with the archived version at Zenodo: https://zenodo.org/records/19068468. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Bioinformatics
University of Copenhagen (DK), Maastricht University Medical Centre (NL), Maastricht University (NL)
Nederlandse Organisatie voor Wetenschappelijk Onderzoek, Maastricht Universitair Medisch Centrum
Openalex Percentile: Top 79%
Genetic Neurodegenerative Diseases
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