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Single-molecule long-read sequencing has been used to improve mRNA isoform identification. However, not all single-molecule long reads represent full transcripts due to incomplete cDNA synthesis and sequencing length limits. This drives a need for long-read transcript assembly. By adding long-read-specific optimizations to Scallop, we developed Scallop-LR, a reference-based long-read transcript assembler. Analyzing 26 PacBio samples, we quantified the benefit of performing transcript assembly on long reads. We demonstrate Scallop-LR identifies more known transcripts and potentially novel isoforms for the human transcriptome than Iso-Seq Analysis and StringTie, indicating that long-read transcript assembly by Scallop-LR can reveal a more complete human transcriptome.

Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads