pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls

Genome Biology

卷:24

Software

Rene Snajder¹  Marc Jan Bonder²  Oliver Stegle³  Adrien Leger⁴ 

[1] Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany;Faculty for Biosciences, Heidelberg University, Heidelberg, Germany;HIDSS4Health, Helmholtz Information and Data Science School for Health, Heidelberg, Germany;

[2] Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany;Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany;

[3] Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany;Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany;Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK;

[4] European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL), Hinxton, Cambridge, UK;Current affiliation: Oxford Nanopore Technologies, Gosling Building, Oxford Science Park, Oxford, UK;

关键词: Nanopore;    Methylation;    meth5;    pycometh;   

DOI  :  10.1186/s13059-023-02917-w

 received in 2022-08-26, accepted in 2023-03-30,  发布年份 2023

来源: Springer

【 摘 要 】

We present pycoMeth, a toolbox to store, manage and analyze DNA methylation calls from long-read sequencing data obtained using the Oxford Nanopore Technologies sequencing platform. Building on a novel, rapid-access, read-level and reference-anchored methylation storage format MetH5, we propose efficient algorithms for haplotype aware, multi-sample consensus segmentation and differential methylation testing. We show that MetH5 is more efficient than existing solutions for storing Oxford Nanopore Technologies methylation calls, and carry out benchmarking for pycoMeth segmentation and differential methylation testing, demonstrating increased performance and sensitivity compared to existing solutions designed for short-read methylation data.

【 授权许可】

CC BY   
© The Author(s) 2023

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