iPAC: a genome-guided assembler of isoforms via phasing and combing paths
iPAC: a genome-guided assembler of isoforms via phasing and combing paths
复制标题
iPAC：通过定相和组合路径进行基因组引导的亚型组装程序
DOI：
10.1093/bioinformatics/btaa052
复制
发表时间：
2020
期刊：
影响因子：
5.8
通讯作者：
Guojun Li
中科院分区：
文献类型：
--
作者：
Ting Yu;Juntao Liu;Xin Gao;Guojun Li
动机
对于广泛应用的RNA-seq数据分析来说，全长转录本的重建是非常重要和具有挑战性的。目前可用的RNA-seq组装器在实际应用中通常受到严重的限制，例如组装精度低以及与最新的比对工具不兼容。
结果
我们介绍iPAC，一种新的基因组指导的组装重建的异构体，它彻底改变了使用配对的末端和测序深度信息通过定相和梳理路径在一个新设计的定相图。在模拟和真实的数据集上进行测试，它在某种程度上上级同类的所有突出的汇编器。特别是，iPAC在恢复低表达转录物方面显着强大，而其他转录物则不然。
可用性
iPAC可在http://sourceforge.net/projects/transassembly/files上免费获得。
补充资料
补充数据可在Bioinformatics在线获得。
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
iPAC is freely available at http://sourceforge.net/projects/transassembly/files.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.