The TransRate workflow. (1) TransRate takes as input one or more de novo transcriptome assemblies and the paired-end reads used to generate them. (2) The reads are aligned to the contigs. (3) Multimapping reads are proportionally assigned to contigs based on the posterior probability that each contig was the true origin of the read. (4) The alignments are evaluated using four discrete score components. (5) The four score components are integrated to generate the TransRate contig score. (6) The TransRate assembly score is calculated from analysis of all contig scores.