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Comparative Transcriptome Profiling of Disruptive Technology, Single- Molecule Direct RNA Sequencing

Author(s):

Chaithra Pradeep, Dharam Nandan, Arya A Das and Dinesh Velayutham*   Pages 1 - 8 ( 8 )

Abstract:


The standard approach for transcriptomic profiling involves high throughput short read sequencing technology, mainly dominated by Illumina. However, the short reads have limitations in transcriptome assembly and to obtain full length transcripts due to the complex nature of transcriptomes with variable length and multiple alternative spliced isoforms. Recent advances in the long read sequencing by the Oxford Nanopore Technologies (ONT) offered both cDNA as well as direct RNA sequencing and has brought a paradigm change in the sequencing technology to greatly improve the assembly and expression estimates. ONT enables molecules to be sequenced without fragmentation resulting in ultra long read length enabling the entire genes and transcripts to be fully characterized. The direct RNA sequencing method in addition circumvents the reverse transcription and amplification steps. In this study, we focus on sensitivity & specificity of the isoform detection using Saccharomyces cerevisiae as model data generated by Illumina, ONT cDNA and ONT direct RNA sequencing technologies. We present mapping metrics and qualitative profile for different pipelines that will enable understanding of these disruptive technologies.

Keywords:

Oxford Nanopore Technologies (ONT), direct RNA sequencing, ONT cDNA, second-generation sequencing (SGS), next generation sequencing (NGS) , third-generation single molecular sequencing (TGS)

Affiliation:

Bioinformatics Team, AgriGenome Labs Pvt Ltd, Kakkanad, Kerala, Bioinformatics Team, AgriGenome Labs Pvt Ltd, Kakkanad, Kerala, Bioinformatics Team, AgriGenome Labs Pvt Ltd, Kakkanad, Kerala, Bioinformatics Team, AgriGenome Labs Pvt Ltd, Kakkanad, Kerala



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