Preprint Article Version 2 This version is not peer-reviewed

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

Version 1 : Received: 12 October 2019 / Approved: 13 October 2019 / Online: 13 October 2019 (15:51:58 CEST)
Version 2 : Received: 7 April 2020 / Approved: 8 April 2020 / Online: 8 April 2020 (06:21:10 CEST)

A peer-reviewed article of this Preprint also exists.

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. 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.

Journal reference: Int. J. Mol. Sci. 2020, 21, 3828
DOI: 10.3390/ijms21113828

Abstract

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 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

Supplementary and Associated Material

Subject Areas

NGS data analysis; bioinformatics pipelines; NGS pipelines

Comments (1)

Comment 1
Received: 8 April 2020
Commenter: Omer An
Commenter's Conflict of Interests: Author
Comment: - New pipelines added
- Manuscript amended accordingly and improved
- Graphical abstract added
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