NGS Processing Technologies and Applications

Participants: Xie Luyu, Zhao Liang, Li Jinyan, Wong Limsoon

Overview

NGS (next-generation sequencing) technologies have become affordable for more applications. However, the data volumes produced also impose very high demands on computing resources to process and use. For example, genome assembly from NGS reads may take hours to complete, and may require processing nodes with terrabyte memory. This impedes applications in practical settings requiring fast turnaround and/or running on typical desktop computers.

In this project, we develop technologies for more efficient processing of NGS data (e.g. compression, error correction, indexing, and assembly), and apply these technologies in real-life applications (e.g. prenatal and neonatal precision medicine).

Selected Publications

NGS processing technologies

• Yuansheng Liu, Hui Peng, Limsoon Wong, Jinyan Li. High-speed and high-ratio referential genome compression. Bioinformatics, 33(21):3364--3372, November 2017. PDF

• Liang Zhao, Qingfeng Chen, Wencui Li, Peng Jiang, Limsoon Wong, Jinyan Li. MapReduce for accurate error correction of next-generation sequencing data. Bioinformatics, 33(23):3844--3851, December 2017. PDF, Source codes

• Peng Jiang, Jie Luo, Yiqi Wang, Pingji Deng, Bertil Schmidt, Xiangjun Tang, Ningjiang Chen, Limsoon Wong, Liang Zhao. kmcEx: Memory-frugal and retrieval-efficient encoding of counted k-mers. Bioinformatics, 35(23):4871--4878, December 2019. PDF, Source codes

• Yuansheng Liu, Limsoon Wong, Jinyan Li. Allowing mutations in maximal mathces boosts genome compression performance. Bioinformatics, 36(18):4675--4681, September 2020. PDF.

• Luyu Xie, Limsoon Wong. PDR: A new genome assembly evaluation metric based on genetics concerns. Bioinformatics, 37(3):289--295, February, 2021. PDF.

  NGS applications

Selected Presentations

• Limsoon Wong. A law of genetic linkage interdicts unlawful assemblies. Keynote address at Workshop on Intelligent Computing and Bioinformatics (ICBio 2018), Xiangtan University, China, 1-2 December 2018. PPT

• Limsoon Wong. A law of genetic linkage interdicts unlawful assembly. Keynote at 5th IASBS Symposium in Biological Sciences, Institute for Advanced Studies in Basic Sciences, Zanjan, Iran, 16 January 2020. PPT

• Limsoon Wong. Genome assembly quality assessment integrating contiguity, completeness, and correctness. Invited talk at IMS Program on Computational Approaches to the Analysis of Biomolecular Sequences, Structures and their Functions and Applications to Biotechnology and Clinical Data Studies, Institute for Mathematical Sciences, Singapore, 23-27 March 2020. PPT

Dissertations

• Xie Luyu, Evaluation and improvement of genome assembly. School of Computing, National University of Singapore, 2020.

Acknowledgements