cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data.
bioRxiv
; 2023 Jul 27.
Article
en En
| MEDLINE
| ID: mdl-37546844
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/.
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Colección:
01-internacional
Banco de datos:
MEDLINE
Idioma:
En
Revista:
BioRxiv
Año:
2023
Tipo del documento:
Article
País de afiliación:
Estados Unidos