Pertea, M. et al. Nat Biotechnol. 33, 290–295 (2015).

Transcriptomes in higher eukaryotes are highly complex, with coding and noncoding transcripts subject to intricate regulation and alternative splicing. High-throughput RNA sequencing (RNA-seq) can rapidly produce short reads that make up a transcriptome, but unambiguous assembly of the correct transcripts is difficult. Pertea et al. developed a de novo read assembly approach that simultaneously assembles transcripts and assesses their expression level. In a comparison with the popular RNA-seq assembly algorithm Cufflinks, StringTie assembled over 50% more transcripts on data from human blood. The researchers also demonstrated its higher accuracy for assembly and quantitation of transcripts—without loss of sensitivity and precision—relative to the accuracies of competing algorithms.