Comparison of the assembly accuracy, measured with precision (%) and the number of matching transcripts, of StringTie2 and Scallop2 using different annotations as the reference.

In each combination (of dataset, aligner, genome build, annotation) the two metrics are averaged over all samples in the dataset. Symbol 〈〉 indicates that one method gets higher on one metric but lower on the other; symbol > indicates that StringTie2 outperforms on both metrics, while raw counts give the number of samples in each category by comparing raw precision and recall. Samples in the 〈〉 category are further compared using the adjusted precision, and the number of samples are merged into either > or adjusted.