Novel transcript discovery in yeast using sequencing reads from Oxford Nanopore Technologies in comparison to Next Generation Sequencing

Abstract

The advent of Oxford Nanopore Technologies is expected to play a pivotal role in near future sequencing studies. Omics data analysis and related processes, currently bound to Next Generation Sequencing, can be now complemented and improved by the rise of Nanopore devices, tools and pipelines. We have herein explored the advantages and limitations of the application of Nanopore technologies for the reconstruction of transcriptomes as well as the discovery of unannotated genes sequences in yeast. Taking Saccharomyces cerevisiae as our focal species, comprehensive pipelines have been developed, optimised and compared with other processing approaches, also generated in-house. The comparisons of newly suggested pipelines with existing Illumina-based strategies are of especial interest. As a result of this investigation project, we provide insights about the impact of different technologies and pipelines for transcriptomics data processing and analysis. At the same time, reproducible code and technical details are made available along with the report.