cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data

Meleshko, D.; Prjbelski, A. D.; Rayko, M.; Tomescu, A. I.; Tilgner, H.; Hajirasouliha, I.

doi:10.1101/2023.07.25.550587

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bioRxiv · 10.1101/2023.07.25.550587

cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data

Meleshko, D.·Prjbelski, A. D.·Rayko, M.·Tomescu, A. I.·Tilgner, H.·Hajirasouliha, I.

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Abstract

MotivationRecent 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. ResultsIn 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. AvailabilitycloudrnaSPAdes is a feature release of a SPAdes assembler and available at https://cab.spbu.ru/software/cloudrnaspades/. Contactdmm2017@med.cornell.edu

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Meleshko, D., Prjbelski, A. D., Rayko, M., Tomescu, A. I., Tilgner, H., Hajirasouliha, I.. 2023-07-27. cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data. https://doi.org/10.1101/2023.07.25.550587

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