TransRate contig score is related to assembly accuracy. Contigs from assemblies of simulated reads from four species (rice, mouse, yeast, and human) were evaluated using TransRate and RSEM-eval. Reciprocal best-BLAST against the true set of transcripts was used to determine the F-score, or reference-based accuracy, of the assembled contig. Each point is a contig in an assembly, with all four assemblies on the same plot. (A) Comparison between TransRate contig score and contig F-score. (B) Comparison between RSEM-eval contig impact score and contig F-score, with contig impact scores below 0 set to the smallest positive value in the data to enable plotting.