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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| Main Authors: | , , , |
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| Format: | Article (Journal) |
| Language: | English |
| Published: |
20 April 2023
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| In: |
Genome biology
Year: 2023, Volume: 24, Pages: 1-19 |
| ISSN: | 1474-760X |
| DOI: | 10.1186/s13059-023-02917-w |
| Online Access: | Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1186/s13059-023-02917-w
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| Author Notes: | Rene Snajder, Adrien Leger, Oliver Stegle and Marc Jan Bonder |
| Summary: | 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. |
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| Item Description: | Gesehen am 17.11.2023 |
| Physical Description: | Online Resource |
| ISSN: | 1474-760X |
| DOI: | 10.1186/s13059-023-02917-w |