iPAC：通过相位和组合路径对异构体进行基因组指导组装的工具。

iPAC: a genome-guided assembler of isoforms via phasing and combing paths.

机构信息

School of Mathematics, Shandong University, Jinan 250100, China.

Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia.

出版信息

Bioinformatics. 2020 May 1;36(9):2712-2717. doi: 10.1093/bioinformatics/btaa052.

DOI:10.1093/bioinformatics/btaa052

PMID:31985799

Abstract

MOTIVATION

Full-length transcript reconstruction is very important and quite challenging for the widely used RNA-seq data analysis. Currently, available RNA-seq assemblers generally suffered from serious limitations in practical applications, such as low assembly accuracy and incompatibility with latest alignment tools.

RESULTS

We introduce iPAC, a new genome-guided assembler for reconstruction of isoforms, which revolutionizes the usage of paired-end and sequencing depth information via phasing and combing paths over a newly designed phasing graph. Tested on both simulated and real datasets, it is to some extent superior to all the salient assemblers of the same kind. Especially, iPAC is significantly powerful in recovery of lowly expressed transcripts while others are not.

AVAILABILITY AND IMPLEMENTATION

iPAC is freely available at http://sourceforge.net/projects/transassembly/files.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

动机

全长转录本重建对于广泛使用的 RNA-seq 数据分析非常重要且极具挑战性。目前，现有的 RNA-seq 组装器在实际应用中普遍存在严重的局限性，例如组装准确性低，与最新的比对工具不兼容。

结果

我们引入了 iPAC，这是一种新的基于基因组指导的异构体重建组装器，它通过在新设计的相位图上对路径进行相位和组合，彻底改变了对配对末端和测序深度信息的利用。在模拟和真实数据集上的测试表明，在某种程度上，它优于所有同类的显著组装器。特别是，iPAC 在恢复低表达转录本方面非常强大，而其他组装器则不行。