The DETONATE package workflow. The DETONATE package consists of two components: RSEM-EVAL and REF-EVAL. Combined, these two components allow for the computation of a variety of evaluation scores for a de novo transcriptome assembly. RSEM-EVAL produces an evaluation score that is based only on an assembly and the set of reads from which it was constructed. When a reference transcript set is available, REF-EVAL may be used to compute a number of reference-based measures. For most measures, REF-EVAL requires only an assembly and a reference transcript set. For weighted measures and measures with respect to an estimated true contig set, REF-EVAL additionally requires the set of reads that were assembled (dashed arrow).