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

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 effi...

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Autores principales: Snajder, Rene, Leger, Adrien, Stegle, Oliver, Bonder, Marc Jan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10120131/
https://www.ncbi.nlm.nih.gov/pubmed/37081487
http://dx.doi.org/10.1186/s13059-023-02917-w
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author Snajder, Rene
Leger, Adrien
Stegle, Oliver
Bonder, Marc Jan
author_facet Snajder, Rene
Leger, Adrien
Stegle, Oliver
Bonder, Marc Jan
author_sort Snajder, Rene
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02917-w.
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spelling pubmed-101201312023-04-22 pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls Snajder, Rene Leger, Adrien Stegle, Oliver Bonder, Marc Jan Genome Biol Software 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02917-w. BioMed Central 2023-04-20 /pmc/articles/PMC10120131/ /pubmed/37081487 http://dx.doi.org/10.1186/s13059-023-02917-w Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Snajder, Rene
Leger, Adrien
Stegle, Oliver
Bonder, Marc Jan
pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls
title pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls
title_full pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls
title_fullStr pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls
title_full_unstemmed pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls
title_short pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls
title_sort pycometh: a toolbox for differential methylation testing from nanopore methylation calls
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10120131/
https://www.ncbi.nlm.nih.gov/pubmed/37081487
http://dx.doi.org/10.1186/s13059-023-02917-w
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AT stegleoliver pycomethatoolboxfordifferentialmethylationtestingfromnanoporemethylationcalls
AT bondermarcjan pycomethatoolboxfordifferentialmethylationtestingfromnanoporemethylationcalls

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