Accurate assembly of multi-end RNA-seq data with Scallop2
Accurate assembly of multi-end RNA-seq data with Scallop2
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DOI：
10.1038/s43588-022-00216-1
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发表时间：
2022-03
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通讯作者：
Qimin Zhang;Qian Shi;Mingfu Shao
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作者：
Qimin Zhang;Qian Shi;Mingfu Shao
现代RNA测序（RNA-seq）方案可以产生多末端数据，其中源自相同转录物的多个读段连接到相同条形码。多末端读段中的长距离信息在对复杂的剪接同种型进行定相中是有益的，但是缺乏利用这种信息的组装算法。在这里，我们介绍Scallop 2，一个基于参考的汇编程序，针对多末端RNA-seq数据进行了优化。Scallop 2的算法核心由三个步骤组成：（1）在拼接图的上下文中，使用算法将多端读段“桥接”到单端定相路径中，（2）采用一种方法通过利用未能桥接的多端读段来细化错误的拼接图，以及（3）将细化的拼接图和桥接的定相路径输送到集成多个相位保持分解的算法中。在两个Smart-seq 3数据集的561个细胞和10个Illumina配对末端RNA-seq样本上进行了测试，与两个流行的组装器（StringTie 2和Scallop）相比，Scallop 2大大提高了组装精度。
Modern RNA-sequencing (RNA-seq) protocols can produce multi-end data, where multiple reads originating from the same transcript are attached to the same barcode. The long-range information in the multi-end reads is beneficial in phasing complicated spliced isoforms, but assembly algorithms that leverage such information are lacking. Here we introduce Scallop2, a reference-based assembler optimized for multi-end RNA-seq data. The algorithmic core of Scallop2 consists of three steps: (1) using an algorithm to ‘bridge’ multi-end reads into single-end phasing paths in the context of a splice graph, (2) employing a method to refine erroneous splice graphs by utilizing multi-end reads that fail to bridge and (3) piping the refined splice graph and bridged phasing paths into an algorithm that integrates multiple phase-preserving decompositions. Tested on 561 cells in two Smart-seq3 datasets and on ten Illumina paired-end RNA-seq samples, Scallop2 substantially improves the assembly accuracy compared with two popular assemblers (StringTie2 and Scallop).