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cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data

Dmitry Meleshko, Andrey D. Prjbelski, Mikhail Raiko, Alexandru I. Tomescu, Hagen Tilgner, Iman Hajirasouliha
doi: https://doi.org/10.1101/2023.07.25.550587
Dmitry Meleshko
1Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine of Cornell University, NY, 10021, USA
2Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, NY, 10021, USA
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  • For correspondence: meleshko.dmitrii@gmail.com
Andrey D. Prjbelski
3Department of Computer Science, University of Helsinki, Finland
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Mikhail Raiko
4Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia, 199004
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Alexandru I. Tomescu
3Department of Computer Science, University of Helsinki, Finland
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Hagen Tilgner
5Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10021, USA
6Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
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Iman Hajirasouliha
2Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, NY, 10021, USA
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Abstract

Motivation Recent advancements in long-read RNA sequencing have enabled the examination of full-length isoforms, previously uncaptured by short-read sequencing methods. An alternative powerful method for studying isoforms is through the use of barcoded short-read RNA reads, for which a barcode indicates whether two short-reads arise from the same molecule or not. Such techniques included the 10x Genomics linked-read based SParse Isoform Sequencing (SPIso-seq), as well as Loop-Seq, or Tell-Seq. Some applications, such as novel-isoform discovery, require very high coverage. Obtaining high coverage using long reads can be difficult, making barcoded RNA-seq data a valuable alternative for this task. However, most annotation pipelines are not able to work with a set of short reads instead of a single transcript, also not able to work with coverage gaps within a molecule if any. In order to overcome this challenge, we present an RNA-seq assembler allowing the determination of the expressed isoform per barcode.

Results In this paper, we present cloudrnaSPAdes, a tool for assembling full-length isoforms from barcoded RNA-seq linked-read data in a reference-free fashion. Evaluating it on simulated and real human data, we found that cloudrnaSPAdes accurately assembles isoforms, even for genes with high isoform diversity.

Availability cloudrnaSPAdes is a feature release of a SPAdes assembler and available at https://cab.spbu.ru/software/cloudrnaspades/.

Contact dmm2017{at}med.cornell.edu

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 27, 2023.
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cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data
Dmitry Meleshko, Andrey D. Prjbelski, Mikhail Raiko, Alexandru I. Tomescu, Hagen Tilgner, Iman Hajirasouliha
bioRxiv 2023.07.25.550587; doi: https://doi.org/10.1101/2023.07.25.550587
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cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data
Dmitry Meleshko, Andrey D. Prjbelski, Mikhail Raiko, Alexandru I. Tomescu, Hagen Tilgner, Iman Hajirasouliha
bioRxiv 2023.07.25.550587; doi: https://doi.org/10.1101/2023.07.25.550587

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