RT Journal Article
SR Electronic
T1 cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2023.07.25.550587
DO 10.1101/2023.07.25.550587
A1 Dmitry Meleshko
A1 Andrey D. Prjbelski
A1 Mikhail Raiko
A1 Alexandru I. Tomescu
A1 Hagen Tilgner
A1 Iman Hajirasouliha
YR 2023
UL http://biorxiv.org/content/early/2023/07/27/2023.07.25.550587.abstract
AB 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.eduCompeting Interest StatementThe authors have declared no competing interest.