Single cell transcriptome sequencing on the Oxford Nanopore platform with ScNapBar
About Christoph Dieterich
Christoph Dieterich received his Ph.D. degree in Bioinformatics from Free University Berlin, Germany, in 2005. He is currently Professor of Bioinformatics and Systems Cardiology at the Medical Faculty of Heidelberg University, and head of the Klaus Tschira Institute for Integrative Computational Cardiology. He is specifically interested in RNA species and network analysis to advance our understanding of cardiovascular health and disease and is active in the field of RNA therapeutics, which will open up new medical options.
The Oxford Nanopore platform offers long-read sequencing and can be integrated with popular single cell sequencing methods, such as the 10x Chromium platform. However, the error-rate of Oxford Nanopore reads poses a challenge in downstream processing (e.g. for cell barcode assignment). We propose a solution to this particular problem, by using a hybrid sequencing approach on Oxford Nanopore and Illumina platforms. Our software ScNapBar enables cell barcode assignment with high accuracy, especially if sequencing saturation is low. ScNapBar uses either unique molecular identifier (UMI) or a naive Bayes probabilistic approach to barcode assignment, depending on the available Illumina sequencing depth.