Shao Mingfu, Kingsford Carl
Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
Nat Biotechnol. 2017 Dec;35(12):1167-1169. doi: 10.1038/nbt.4020. Epub 2017 Nov 13.
We introduce Scallop, an accurate reference-based transcript assembler that improves reconstruction of multi-exon and lowly expressed transcripts. Scallop preserves long-range phasing paths extracted from reads, while producing a parsimonious set of transcripts and minimizing coverage deviation. On 10 human RNA-seq samples, Scallop produces 34.5% and 36.3% more correct multi-exon transcripts than StringTie and TransComb, and respectively identifies 67.5% and 52.3% more lowly expressed transcripts. Scallop achieves higher sensitivity and precision than previous approaches over a wide range of coverage thresholds.
我们介绍了Scallop，这是一种基于参考的精确转录本组装工具，可改进多外显子和低表达转录本的重建。Scallop保留了从读取中提取的长程相位路径，同时生成一组简约的转录本并最小化覆盖偏差。在10个人类RNA测序样本上，Scallop产生的正确多外显子转录本比StringTie和TransComb分别多34.5%和36.3%，并且分别多识别出67.5%和52.3%的低表达转录本。在广泛的覆盖阈值范围内，Scallop比以前的方法具有更高的灵敏度和精度。
