TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
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DOI：
10.1186/gb-2013-14-4-r36
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发表时间：
2013-04-25
期刊：
影响因子：
12.3
通讯作者：
Salzberg SL
中科院分区：
文献类型：
--
作者：
Kim D;Pertea G;Trapnell C;Pimentel H;Kelley R;Salzberg SL
TopHat是一种用于RNA序列（RNA-seq）实验的流行剪接比对器。在本文中，我们描述了TopHat 2，它结合了许多重大的增强TopHat。TopHat 2可以比对由最新测序技术产生的各种长度的读段，同时允许相对于参考基因组的可变长度indel。除了从头剪接比对之外，TopHat 2还可以跨融合断裂比对读段，这可能发生在基因组易位之后。TopHat 2结合了识别新剪接位点的能力与直接映射到已知转录本的能力，产生灵敏和准确的比对，即使是高度重复的基因组或存在假基因的情况下。TopHat 2可在http://ccb.jhu.edu/software/tophat上获取。
TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. TopHat2 can align reads of various lengths produced by the latest sequencing technologies, while allowing for variable-length indels with respect to the reference genome. In addition to de novo spliced alignment, TopHat2 can align reads across fusion breaks, which can occur after genomic translocations. TopHat2 combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes. TopHat2 is available at http://ccb.jhu.edu/software/tophat.
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