cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data.
cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data.
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cloudrnaSPAdes：使用批量条形码 RNA 测序数据进行异构体组装。
DOI：
10.1101/2023.07.25.550587
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Hajirasouliha,Iman
中科院分区：
文献类型：
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作者：
Meleshko,Dmitry;Prjbelski,AndreyD;Raiko,Mikhail;Tomescu,AlexandruI;Tilgner,Hagen;Hajirasouliha,Iman
最近在长读RNA测序方面的进展使得能够检查全长同种型，以前未被短读测序方法捕获。研究同种型的另一种有效方法是通过使用条形码化的短读段RNA读段，其中条形码指示两个短读段是否来自同一分子。这些技术包括基于IOx基因组学连接读取的SParse同种型测序（SPIso-seq），以及环测序或Tell-Seq。一些应用，如新的异构体发现，需要非常高的覆盖率。使用长读段获得高覆盖率可能很困难，这使得条形码RNA-seq数据成为这项任务的有价值的替代方案。然而，大多数注释流水线不能与一组短读段而不是单个转录物一起工作，也不能与分子内的覆盖缺口（如果有的话）一起工作。为了克服这一挑战，我们提出了一个RNA-seq汇编程序，允许每个barcodes.ResultsIn这篇文章中，我们presentcloudrnaSPAdes，一个工具，用于组装全长异构体从条形码RNA-seq连接读取数据在一个参考的自由时尚的表达亚型的测定。通过对模拟和真实的人类数据进行评估，我们发现cloudrnaSPAdes可以准确地组装异构体，即使是具有高度异构体多样性的基因。可用性和实现cloudrnaSPAdes是SPAdes组装程序的一个功能版本，本文使用的版本可以在https://github.com/1dayac/cloudrnaSPAdes-release上获得。
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 that allows the determination of the expressed isoform per barcode.ResultsIn this article, we presentcloudrnaSPAdes, 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 thatcloudrnaSPAdesaccurately assembles isoforms, even for genes with high isoform diversity.Availability and implementationcloudrnaSPAdes is a feature release of a SPAdes assembler and version used for this article is available at https://github.com/1dayac/cloudrnaSPAdes-release.