Accurate assembly of transcripts through phase-preserving graph decomposition

Corresponding author: Carl Kingsford

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.

作者开发了一套新的转录组组装软件Scallop，其可以提高多外显子和低表达量转录本的组装，用人类转录组的数据显示要比StringTie和TransComb的组装效果好。

研究方向：基因组组装；染色质结构与功能；蛋白互作与网络。

doi: 10.1038/nbt.4020