Msuite2: All-in-one DNA methylation data analysis toolkit with enhanced usability and performance
DNA methylation is an important epigenetic regulator that plays crucial roles in various biological processes. Recent developments in experimental approaches and dramatic expansion of sequencing capacities have imposed new challenges in the analysis of large-scale, cross-species DNA methylation data...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-01-01
|
| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037022000800 |
| _version_ | 1797978225643618304 |
|---|---|
| author | Lishi Li Yunyun An Li Ma Mengqi Yang Pengxiang Yuan Xiaojian Liu Xin Jin Yu Zhao Songfa Zhang Xin Hong Kun Sun |
| author_facet | Lishi Li Yunyun An Li Ma Mengqi Yang Pengxiang Yuan Xiaojian Liu Xin Jin Yu Zhao Songfa Zhang Xin Hong Kun Sun |
| author_sort | Lishi Li |
| collection | DOAJ |
| description | DNA methylation is an important epigenetic regulator that plays crucial roles in various biological processes. Recent developments in experimental approaches and dramatic expansion of sequencing capacities have imposed new challenges in the analysis of large-scale, cross-species DNA methylation data. Hence, user-friendly toolkits with high usability and performance are in urgent need. In this work, we present Msuite2, an easy-to-use, all-in-one, and universal toolkit for DNA methylation data analysis and visualization with high flexibility, usability, and performance. Msuite2 is among the fastest tools in read alignment (in particular, it runs as much as 5x faster than its predecessor, Msuite1) with low computing resource usage. In addition, Msuite2 shows both balanced and high performance in terms of mapping efficiency and accuracy, demonstrating high potential to facilitate the investigation and application of large-scale DNA methylation analysis in various biomedical studies. Msuite2 is freely available at https://github.com/hellosunking/Msuite2/. |
| first_indexed | 2024-04-11T05:20:28Z |
| format | Article |
| id | doaj.art-80b3cefe516647ad96d237ff5a4b9f7d |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:20:28Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-80b3cefe516647ad96d237ff5a4b9f7d2022-12-24T04:51:41ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-012012711276Msuite2: All-in-one DNA methylation data analysis toolkit with enhanced usability and performanceLishi Li0Yunyun An1Li Ma2Mengqi Yang3Pengxiang Yuan4Xiaojian Liu5Xin Jin6Yu Zhao7Songfa Zhang8Xin Hong9Kun Sun10School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, ChinaInstitute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, ChinaInstitute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, ChinaInstitute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, ChinaInstitute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, ChinaInstitute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, ChinaBGI-Shenzhen, Shenzhen 518083, Guangdong, China; School of Medicine, South China University of Technology, Guangzhou 510006, Guangdong, ChinaSchool of Medicine, Sun Yat-sen University, Guangzhou 510080, ChinaWomen's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, Zhejiang, China; Corresponding authors.Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China; Corresponding authors.Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; Corresponding authors.DNA methylation is an important epigenetic regulator that plays crucial roles in various biological processes. Recent developments in experimental approaches and dramatic expansion of sequencing capacities have imposed new challenges in the analysis of large-scale, cross-species DNA methylation data. Hence, user-friendly toolkits with high usability and performance are in urgent need. In this work, we present Msuite2, an easy-to-use, all-in-one, and universal toolkit for DNA methylation data analysis and visualization with high flexibility, usability, and performance. Msuite2 is among the fastest tools in read alignment (in particular, it runs as much as 5x faster than its predecessor, Msuite1) with low computing resource usage. In addition, Msuite2 shows both balanced and high performance in terms of mapping efficiency and accuracy, demonstrating high potential to facilitate the investigation and application of large-scale DNA methylation analysis in various biomedical studies. Msuite2 is freely available at https://github.com/hellosunking/Msuite2/.http://www.sciencedirect.com/science/article/pii/S2001037022000800CpG dinucleotideBisulfite treatmentData visualization |
| spellingShingle | Lishi Li Yunyun An Li Ma Mengqi Yang Pengxiang Yuan Xiaojian Liu Xin Jin Yu Zhao Songfa Zhang Xin Hong Kun Sun Msuite2: All-in-one DNA methylation data analysis toolkit with enhanced usability and performance Computational and Structural Biotechnology Journal CpG dinucleotide Bisulfite treatment Data visualization |
| title | Msuite2: All-in-one DNA methylation data analysis toolkit with enhanced usability and performance |
| title_full | Msuite2: All-in-one DNA methylation data analysis toolkit with enhanced usability and performance |
| title_fullStr | Msuite2: All-in-one DNA methylation data analysis toolkit with enhanced usability and performance |
| title_full_unstemmed | Msuite2: All-in-one DNA methylation data analysis toolkit with enhanced usability and performance |
| title_short | Msuite2: All-in-one DNA methylation data analysis toolkit with enhanced usability and performance |
| title_sort | msuite2 all in one dna methylation data analysis toolkit with enhanced usability and performance |
| topic | CpG dinucleotide Bisulfite treatment Data visualization |
| url | http://www.sciencedirect.com/science/article/pii/S2001037022000800 |
| work_keys_str_mv | AT lishili msuite2allinonednamethylationdataanalysistoolkitwithenhancedusabilityandperformance AT yunyunan msuite2allinonednamethylationdataanalysistoolkitwithenhancedusabilityandperformance AT lima msuite2allinonednamethylationdataanalysistoolkitwithenhancedusabilityandperformance AT mengqiyang msuite2allinonednamethylationdataanalysistoolkitwithenhancedusabilityandperformance AT pengxiangyuan msuite2allinonednamethylationdataanalysistoolkitwithenhancedusabilityandperformance AT xiaojianliu msuite2allinonednamethylationdataanalysistoolkitwithenhancedusabilityandperformance AT xinjin msuite2allinonednamethylationdataanalysistoolkitwithenhancedusabilityandperformance AT yuzhao msuite2allinonednamethylationdataanalysistoolkitwithenhancedusabilityandperformance AT songfazhang msuite2allinonednamethylationdataanalysistoolkitwithenhancedusabilityandperformance AT xinhong msuite2allinonednamethylationdataanalysistoolkitwithenhancedusabilityandperformance AT kunsun msuite2allinonednamethylationdataanalysistoolkitwithenhancedusabilityandperformance |