Msuite: A High-Performance and Versatile DNA Methylation Data-Analysis Toolkit
Summary: DNA methylation is a pervasive and important epigenetic regulator in mammalian genome. For DNA methylome profiling, emerging bisulfite-free methods have demonstrated desirable superiority over the conventional bisulfite-treatment-based approaches, although current analysis software could no...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2020-11-01
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| Series: | Patterns |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666389920301689 |
| _version_ | 1819172586052911104 |
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| author | Kun Sun Lishi Li Li Ma Yu Zhao Lin Deng Huating Wang Hao Sun |
| author_facet | Kun Sun Lishi Li Li Ma Yu Zhao Lin Deng Huating Wang Hao Sun |
| author_sort | Kun Sun |
| collection | DOAJ |
| description | Summary: DNA methylation is a pervasive and important epigenetic regulator in mammalian genome. For DNA methylome profiling, emerging bisulfite-free methods have demonstrated desirable superiority over the conventional bisulfite-treatment-based approaches, although current analysis software could not make full use of their advantages. In this work, we present Msuite, an easy-to-use, all-in-one data-analysis toolkit. Msuite implements a unique 4-letter analysis mode specifically optimized for emerging protocols; it also integrates quality controls, methylation call, and data visualizations. Msuite demonstrates substantial performance improvements over current state-of-the-art tools as well as fruitful functionalities, thus holding the potential to serve as an optimal toolkit to facilitate DNA methylome studies. Source codes and testing datasets for Msuite are freely available at https://github.com/hellosunking/Msuite/. The Bigger Picture: DNA methylation is an essential epigenetic modification responsible for many biological regulation pathways. Despite the fact that various high-throughput methods have been developed for base-resolution DNA methylome profiling, DNA methylation data analysis remains a complex and challenging task. Here, we present Msuite, which has integrated quality control, read alignment, methylation call, and fruitful data-visualization functionalities, aiming to offer an all-in-one package for most of the current DNA methylation profiling assays. Msuite also provides dedicated support for emerging bisulfite-free protocols and outperforms the current tools in terms of higher accuracy and lower computational resource requirement. Hence, Msuite could serve as the optimal toolkit for DNA methylation data analysis as well as facilitating the popularization of emerging bisulfite-free protocols. |
| first_indexed | 2024-12-22T20:09:32Z |
| format | Article |
| id | doaj.art-3b44ea6126f84c099926d560fd5c2484 |
| institution | Directory Open Access Journal |
| issn | 2666-3899 |
| language | English |
| last_indexed | 2024-12-22T20:09:32Z |
| publishDate | 2020-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Patterns |
| spelling | doaj.art-3b44ea6126f84c099926d560fd5c24842022-12-21T18:14:04ZengElsevierPatterns2666-38992020-11-0118100127Msuite: A High-Performance and Versatile DNA Methylation Data-Analysis ToolkitKun Sun0Lishi Li1Li Ma2Yu Zhao3Lin Deng4Huating Wang5Hao Sun6Shenzhen Bay Laboratory, Shenzhen 518132, China; Corresponding authorShenzhen Bay Laboratory, Shenzhen 518132, China; Peking University Shenzhen Graduate School, Shenzhen 518055, ChinaShenzhen Bay Laboratory, Shenzhen 518132, ChinaSchool of Medicine, Sun Yat-sen University, Guangzhou 510080, ChinaShenzhen Bay Laboratory, Shenzhen 518132, ChinaLi Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong SAR 999077, ChinaLi Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR 999077, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR 999077, ChinaSummary: DNA methylation is a pervasive and important epigenetic regulator in mammalian genome. For DNA methylome profiling, emerging bisulfite-free methods have demonstrated desirable superiority over the conventional bisulfite-treatment-based approaches, although current analysis software could not make full use of their advantages. In this work, we present Msuite, an easy-to-use, all-in-one data-analysis toolkit. Msuite implements a unique 4-letter analysis mode specifically optimized for emerging protocols; it also integrates quality controls, methylation call, and data visualizations. Msuite demonstrates substantial performance improvements over current state-of-the-art tools as well as fruitful functionalities, thus holding the potential to serve as an optimal toolkit to facilitate DNA methylome studies. Source codes and testing datasets for Msuite are freely available at https://github.com/hellosunking/Msuite/. The Bigger Picture: DNA methylation is an essential epigenetic modification responsible for many biological regulation pathways. Despite the fact that various high-throughput methods have been developed for base-resolution DNA methylome profiling, DNA methylation data analysis remains a complex and challenging task. Here, we present Msuite, which has integrated quality control, read alignment, methylation call, and fruitful data-visualization functionalities, aiming to offer an all-in-one package for most of the current DNA methylation profiling assays. Msuite also provides dedicated support for emerging bisulfite-free protocols and outperforms the current tools in terms of higher accuracy and lower computational resource requirement. Hence, Msuite could serve as the optimal toolkit for DNA methylation data analysis as well as facilitating the popularization of emerging bisulfite-free protocols.http://www.sciencedirect.com/science/article/pii/S2666389920301689bisulfite sequencingbisulfite-freeCpG dinucleotidequality controldata visualizationimprinting gene |
| spellingShingle | Kun Sun Lishi Li Li Ma Yu Zhao Lin Deng Huating Wang Hao Sun Msuite: A High-Performance and Versatile DNA Methylation Data-Analysis Toolkit Patterns bisulfite sequencing bisulfite-free CpG dinucleotide quality control data visualization imprinting gene |
| title | Msuite: A High-Performance and Versatile DNA Methylation Data-Analysis Toolkit |
| title_full | Msuite: A High-Performance and Versatile DNA Methylation Data-Analysis Toolkit |
| title_fullStr | Msuite: A High-Performance and Versatile DNA Methylation Data-Analysis Toolkit |
| title_full_unstemmed | Msuite: A High-Performance and Versatile DNA Methylation Data-Analysis Toolkit |
| title_short | Msuite: A High-Performance and Versatile DNA Methylation Data-Analysis Toolkit |
| title_sort | msuite a high performance and versatile dna methylation data analysis toolkit |
| topic | bisulfite sequencing bisulfite-free CpG dinucleotide quality control data visualization imprinting gene |
| url | http://www.sciencedirect.com/science/article/pii/S2666389920301689 |
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