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. 2020 May 28;21(11):3828.
doi: 10.3390/ijms21113828.

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

Omer An  1 , Kar-Tong Tan  1 , Ying Li  1 , Jia Li  1 , Chan-Shuo Wu  1 , Bin Zhang  1 , Leilei Chen  1   2 , Henry Yang  1
Affiliations

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

Omer An et al. Int J Mol Sci. .

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 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.

Keywords: NGS data analysis; NGS pipelines; bioinformatics pipelines.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Website Framework of CSI NGS Portal. The middle panel shows the logical flow of the website from top to the bottom, whereas the automated steps of the data transitions from one page to another are described in the left panel, and the function of each page expecting user input/action is given in the right panel. formula image: Logical flow; formula image: Automated step; formula image: Page function.
Figure 2
Figure 2
Website Interface and Usage of CSI NGS Portal. (a) Upload page, (b) Annotation page, (c) Submit page, (d) Jobs page, and (e) Browse page. Key features and usage information are highlighted in text boxes. Further details on the quotas, rules and usage instructions are given on the “README” sections on the website.
Figure 2
Figure 2
Website Interface and Usage of CSI NGS Portal. (a) Upload page, (b) Annotation page, (c) Submit page, (d) Jobs page, and (e) Browse page. Key features and usage information are highlighted in text boxes. Further details on the quotas, rules and usage instructions are given on the “README” sections on the website.
See this image and copyright information in PMC

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