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

Snakemake pipeline integrating, from Oxford Nanopore whole-genome sequencing, the genetic and methylation analysis of all classes of repeats.

The human genome is dominated by repetitive DNA, whose genetic and epigenetic variation contributes to gene regulation, genome stability and disease. Long-read sequencing now enables large-scale, haplotype-resolved and methylation-informative analysis, including in complex regions that were previously inaccessible, yet no single tool covered the full spectrum of repeat types. The authors present ECHO, a user-friendly Snakemake-based pipeline for the (epi)genomic characterisation of human repetitive elements using Oxford Nanopore sequencing. It provides a reproducible, scalable framework for end-to-end analysis of whole-genome nanopore data, supporting both integrative and tailored analyses of the repeatome. The code is freely available on GitHub, with an archived version on Zenodo.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

The contribution is integrative rather than algorithmic: assembling into a single reproducible pipeline what was previously stitched together by hand across several tools, while keeping the methylation information natively carried by nanopore reads. For a laboratory moving to long-read sequencing, this is the kind of building block that decides routine feasibility, since repeat expansions and their methylation status are a daily need. The abstract reports no performance metric and no validation on a patient cohort, however: this is a tool made available, not yet a demonstration of diagnostic yield.

Analysis by Dr Thibaut Benquey