Abstract
Oxford Nanopore (ONT) is a leading long-read technology which has been revolutionizing transcriptome analysis through its capacity to sequence the majority of transcripts from end-to-end. This has greatly increased our ability to study the diversity of transcription mechanisms such as transcription initiation, termination, and alternative splicing. However, ONT still suffers from high error rates which have thus far limited its scope to reference-based analyses. When a reference is not available or is not a viable option due to reference-bias, error correction is a crucial step towards the reconstruction of the sequenced transcripts and downstream sequence analysis of transcripts. In this paper, we present a novel computational method to error correct ONT cDNA sequencing data, called isONcorrect. IsONcorrect is able to jointly use all isoforms from a gene during error correction, thereby allowing it to correct reads at low sequencing depths. We are able to obtain a median accuracy of 98.9–99.6%, demonstrating the feasibility of applying cost-effective cDNA full transcript length sequencing for reference-free transcriptome analysis.
Highlights
Oxford Nanopore (ONT) is a leading long-read technology which has been revolutionizing transcriptome analysis through its capacity to sequence the majority of transcripts from endto-end
We present a method for error correction transcriptome cDNA ONT data that reduce the error rate to about 1%, thereby demonstrating the feasibility of applying costeffective cDNA full transcript length sequencing for referencefree transcriptome analysis
We presented a novel computational tool isONcorrect to error correct cDNA reads from Oxford Nanopore Technologies
Summary
Oxford Nanopore (ONT) is a leading long-read technology which has been revolutionizing transcriptome analysis through its capacity to sequence the majority of transcripts from endto-end. The Oxford Nanopore (ONT) platform is a leading technology for long-read transcriptome sequencing, due to its portability, low cost, and high throughput[6,7] It has enabled the study of alternative splicing patterns[8], allele-specific typing[3], RNA modifications[6,9,10], the discovery of novel isoforms[6,11,12], and species identification in metatranscriptomic samples[13]. We present a method for error correction transcriptome cDNA ONT data that reduce the error rate to about 1%, thereby demonstrating the feasibility of applying costeffective cDNA full transcript length sequencing for referencefree transcriptome analysis. Our method opens the door for much broader application of ONT transcriptome sequencing
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