A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes

A platform for highly parallel direct sequencing of native RNA strands was recently described by Oxford Nanopore Technologies (ONT); in order to assess overall performance in transcript-level investigations, the technology was applied for sequencing sets of synthetic transcripts as well as a yeast transcriptome. However, despite initial efforts it remains crucial to further investigate characteristics of ONT native RNA sequencing when applied to much more complex transcriptomes. Here we thus undertook extensive native RNA sequencing of polyA+ RNA from two human cell lines, and thereby analysed ~5.2 million aligned native RNA reads which consisted of a total of ~4.6 billion bases. To enable informative comparisons, we also performed relevant ONT direct cDNA- and Illumina-sequencing. We find that while native RNA sequencing does enable some of the anticipated advantages, key unexpected aspects hamper its performance, most notably the quite frequent inability to obtain full-length transcripts from single reads, as well as difficulties to unambiguously infer their true transcript of origin. While characterising issues that need to be addressed when investigating more complex transcriptomes, our study highlights that with some defined improvements, native RNA sequencing could be an important addition to the mammalian transcriptomics toolbox.