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Article

CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing

1
Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
2
Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2020, 21(11), 3828; https://doi.org/10.3390/ijms21113828
Received: 15 April 2020 / Revised: 24 May 2020 / Accepted: 26 May 2020 / Published: 28 May 2020
(This article belongs to the Special Issue Data Analysis and Integration in Cancer Research 2.0)
Next-generation sequencing (NGS) has been a widely-used technology in biomedical research for understanding the role of molecular genetics of cells in health and disease. A variety of computational tools have been developed to analyse the vastly growing NGS data, which often require bioinformatics skills, tedious work and a significant amount of time. To facilitate data processing steps minding the gap between biologists and bioinformaticians, we developed CSI NGS Portal, an online platform which gathers established bioinformatics pipelines to provide fully automated NGS data analysis and sharing in a user-friendly website. The portal currently provides 16 standard pipelines for analysing data from DNA, RNA, smallRNA, ChIP, RIP, 4C, SHAPE, circRNA, eCLIP, Bisulfite and scRNA sequencing, and is flexible to expand with new pipelines. The users can upload raw data in FASTQ format and submit jobs in a few clicks, and the results will be self-accessible via the portal to view/download/share in real-time. The output can be readily used as the final report or as input for other tools depending on the pipeline. Overall, CSI NGS Portal helps researchers rapidly analyse their NGS data and share results with colleagues without the aid of a bioinformatician. The portal is freely available at: https://csibioinfo.nus.edu.sg/csingsportal. View Full-Text
Keywords: NGS data analysis; bioinformatics pipelines; NGS pipelines NGS data analysis; bioinformatics pipelines; NGS pipelines
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MDPI and ACS Style

An, O.; Tan, K.-T.; Li, Y.; Li, J.; Wu, C.-S.; Zhang, B.; Chen, L.; Yang, H. CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing. Int. J. Mol. Sci. 2020, 21, 3828. https://doi.org/10.3390/ijms21113828

AMA Style

An O, Tan K-T, Li Y, Li J, Wu C-S, Zhang B, Chen L, Yang H. CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing. International Journal of Molecular Sciences. 2020; 21(11):3828. https://doi.org/10.3390/ijms21113828

Chicago/Turabian Style

An, Omer, Kar-Tong Tan, Ying Li, Jia Li, Chan-Shuo Wu, Bin Zhang, Leilei Chen, and Henry Yang. 2020. "CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing" International Journal of Molecular Sciences 21, no. 11: 3828. https://doi.org/10.3390/ijms21113828

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