Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed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, however, they often require bioinformatics skills and tedious work to handle with. Moreover, processing raw data such as genome alignment and expression quantification consume a significant amount of time before having the data ready for downstream analyses. 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, developed in PHP and JavaScript with an integrated MariaDB database running on a dedicated Linux server. The portal currently provides 14 standard pipelines for analysing NGS data from DNA, RNA, smallRNA, ChIP, RIP, 4C, SHAPE, circRNA, eCLIP and Bisulfite sequencing, and is flexible to expand with new and customised pipelines. The users can upload raw data in fastq format and submit jobs for the desired analyses 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 an input for other tools depending on the pipeline. Overall, CSI NGS Portal helps researchers rapidly analyse their NGS data, share with colleagues and keep it organised without the aid of a bioinformatician. The website is freely available at: https://csibioinfo.nus.edu.sg/csingsportal

Supplementary and Associated Material

Subject Areas

NGS data analysis; bioinformatics pipelines

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