StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
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DOI：
10.1038/nbt.3122
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发表时间：
2015-03
影响因子：
46.9
通讯作者：
Salzberg SL
中科院分区：
文献类型：
--
作者：
Pertea M;Pertea GM;Antonescu CM;Chang TC;Mendell JT;Salzberg SL
用于转录组测序的方法通常产生超过2亿个短序列。我们介绍了StringTie，这是一种计算方法，它应用了最初在优化理论中开发的网络流算法，以及可选的从头组装，将这些复杂的数据集组装成转录本。当用于分析模拟和真实数据集时，与其他领先的转录本组装程序（包括Cufflinks， IsoLasso， Scripture和Traph）相比，StringTie产生更完整和准确的基因重建和更好的表达水平估计。例如，在人类血液的9000万次读取中，StringTie正确地组装了10990个转录本，而第二好的组装是通过袖扣组装了7187个转录本，这增加了53%的转录本组装。在模拟数据集上，StringTie正确地组装了7559个转录本，比Cufflinks组装的6310个转录本多20%。除了生成更完整的转录组组装外，与其他组装软件（包括Cufflinks）相比，StringTie在迄今为止测试的所有数据集上运行得更快。
Methods used to sequence the transcriptome often produce more than 200 million short sequences. We introduce StringTie, a computational method that applies a network flow algorithm originally developed in optimization theory, together with optional de novo assembly, to assemble these complex data sets into transcripts. When used to analyze both simulated and real data sets, StringTie produces more complete and accurate reconstructions of genes and better estimates of expression levels, compared with other leading transcript assembly programs including Cufflinks, IsoLasso, Scripture and Traph. For example, on 90 million reads from human blood, StringTie correctly assembled 10,990 transcripts, whereas the next best assembly was of 7,187 transcripts by Cufflinks, which is a 53% increase in transcripts assembled. On a simulated data set, StringTie correctly assembled 7,559 transcripts, which is 20% more than the 6,310 assembled by Cufflinks. As well as producing a more complete transcriptome assembly, StringTie runs faster on all data sets tested to date compared with other assembly software, including Cufflinks.