TALC: Transcript-level Aware Long-read Correction

TALC: Transcript-level Aware Long-read Correction

Lucile Broseus, Aubin Thomas, Andrew J Oldfield, Dany Severac, Emeric Dubois, William Ritchie

Bioinformatics, btaa634, https://doi.org/10.1093/bioinformatics/btaa634

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16 July 2020

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Abstract

Motivation

Long-read sequencing technologies are invaluable for determining complex RNA transcript architectures but are error-prone. Numerous ‘hybrid correction’ algorithms have been developed for genomic data that correct long reads by exploiting the accuracy and depth of short reads sequenced from the same sample. These algorithms are not suited for correcting more complex transcriptome sequencing data.

Results

We have created a novel reference-free algorithm called Transcript-level Aware Long-Read Correction (TALC) which models changes in RNA expression and isoform representation in a weighted De Bruijn graph to correct long reads from transcriptome studies. We show that transcript-level aware correction by TALC improves the accuracy of the whole spectrum of downstream RNA-seq applications and is thus necessary for transcriptome analyses that use long read technology.

Availability and implementation

TALC is implemented in C++ and available at https://github.com/lbroseus/TALC.

Supplementary information

Supplementary data are available at Bioinformatics online.

露西尔·布罗斯（Lucile Broseus ） 奥宾·托马斯（Aubin Thomas ） 安德鲁·奥德菲尔德Ĵ ， 丹妮·塞韦拉克（Dany Severac）， Emeric Dubois ， 威廉·里奇

生物信息学，btaa634，https: //doi.org/10.1093/bioinformatics/btaa634

发布时间：

 

2020年7月16日

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抽象

动机

长读的测序技术对于确定复杂的RNA转录物构架非常宝贵，但容易出错。已经开发出许多用于基因组数据的“杂交校正”算法，这些算法通过利用从同一样品测序的短读数的准确性和深度来校正长读数。这些算法不适合校正更复杂的转录组测序数据。

结果

我们创建了一个新颖的无参考算法，称为转录水平感知长读校正（TALC），该算法可对加权De Bruijn图中RNA表达和同工型表示的变化进行建模，以纠正转录组研究中的长读。我们显示，通过TALC进行的转录水平感知校正可提高下游RNA-seq应用程序的整个光谱的准确性，因此对于使用长读技术的转录组分析是必需的。

可用性和实施

TALC是用C ++实现的，可从https://github.com/lbroseus/TALC获得。

补充资料

补充数据可从生物信息学在线获得。