CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing. (Int J Mol Sci, May 2020)

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

Author Information

1Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.
2Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore.

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 bioinformatics.

The portal is freely available here.

Keywords: NGS data analysis; NGS pipelines; bioinformatics pipelines.
PMID: 32481589 DOI: 10.3390/ijms21113828