Improved nanopore read accuracy enables single-cell RNA sequencing

High-throughput short-read sequencing has revolutionized how transcriptomes are quantified and annotated. However, while Illumina short-read sequencers can be used to analyze entire transcriptomes down to the level of individual splicing events with great accuracy, they fall short of analyzing how these individual events are combined into complete RNA transcript isoforms. Because of this shortfall, long-distance information is required to complement short-read sequencing to analyze transcriptomes on the level of full-length RNA transcript isoforms. While long-read sequencing technology can provide this long-distance information, there are issues with both Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) long-read sequencing technologies that prevent their widespread adoption. Briefly, PacBio sequencers produce low numbers of reads with high accuracy, while ONT sequencers produce higher numbers of reads with lower accuracy.

Researchers from UCSC introduce and validate a long-read ONT-based sequencing method. At the same cost, their Rolling Circle Amplification to Concatemeric Consensus (R2C2) method generates more accurate reads of full-length RNA transcript isoforms than any other available long-read sequencing method. These reads can then be used to generate isoform-level transcriptomes for both genome annotation and differential expression analysis in bulk or single-cell samples.

R2C2 method overview

rna-seq

cDNA is circularized using Gibson Assembly, amplified using RCA, and sequenced using the ONT MinION. The resulting raw reads are split into subreads containing full-length or partial cDNA sequences, which are combined into an accurate consensus sequence using our C3POa workflow, which relies on a custom algorithm to detect DNA splints as well as poaV2 and racon.

Volden R, Palmer T, Byrne A, Cole C, Schmitz RJ, Green RE, Vollmers C. (2018) Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA. Proc Natl Acad Sci USA [Epub ahead of print]. [article]

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