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Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis. | LitMetric

Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis.

Nat Commun

Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, USA.

Published: January 2021

AI Article Synopsis

Article 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.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7782715PMC
http://dx.doi.org/10.1038/s41467-020-20340-8DOI Listing

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