cloudrnaSPAdes: isoform assembly using bulk barcoded RNA sequencing data

TL;DR

cloudrnaSPAdes is a tool that assembles full-length RNA isoforms from barcoded RNA sequencing data without needing a reference genome.

Contribution

cloudrnaSPAdes introduces a reference-free method for isoform assembly from barcoded RNA-seq data.

Findings

cloudrnaSPAdes accurately assembles isoforms from simulated and real human data.

The tool performs well even for genes with high isoform diversity.

Abstract

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 that allows the determination of the expressed isoform per barcode.

In this article, 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.

cloudrnaSPAdes is a feature release of a SPAdes assembler and version used for this article is available at https://github.com/1dayac/cloudrnaSPAdes-release.

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