Rxivist logo

Quantifying the Benefit Offered by Transcript Assembly on Single-Molecule Long Reads

By Laura H Tung, Mingfu Shao, Carl Kingsford

Posted 10 May 2019
bioRxiv DOI: 10.1101/632703

Third-generation sequencing technologies benefit transcriptome analysis by generating longer sequencing reads. However, not all single-molecule long reads represent full transcripts due to incomplete cDNA synthesis and the sequencing length limit of the platform. This drives a need for long read transcript assembly. We quantify the benefit that can be achieved by using a transcript assembler on long reads. Adding long-read-specific algorithms, we evolved Scallop to make Scallop-LR, a long-read transcript assembler, to handle the computational challenges arising from long read lengths and high error rates. Analyzing 26 SRA PacBio datasets using Scallop-LR, Iso-Seq Analysis, and StringTie, we quantified the amount by which assembly improved Iso-Seq results. Through combined evaluation methods, we found that Scallop-LR identifies 2100-4000 more (for 18 human datasets) or 1100-2200 more (for eight mouse datasets) known transcripts than Iso-Seq Analysis, which does not do assembly. Further, Scallop-LR finds 2.4-4.4 times more potentially novel isoforms than Iso-Seq Analysis for the human and mouse datasets. StringTie also identifies more transcripts than Iso-Seq Analysis. Adding long-read-specific optimizations in Scallop-LR increases the numbers of predicted known transcripts and potentially novel isoforms for the human transcriptome compared to several recent short-read assemblers (e.g. StringTie). Our findings indicate that transcript assembly by Scallop-LR can reveal a more complete human transcriptome.

Download data

  • Downloaded 494 times
  • Download rankings, all-time:
    • Site-wide: 33,131 out of 92,757
    • In bioinformatics: 4,236 out of 8,680
  • Year to date:
    • Site-wide: 44,077 out of 92,757
  • Since beginning of last month:
    • Site-wide: 32,368 out of 92,757

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News