Heat map showing for each data set (column) and each assembler (row) the calculated metric score (MS) (detailed definition in the Methods). The assembly tools are clustered based on their achieved MS over all data sets. The MS for 1 assembly tool and a single data set is based on 20 pre-selected metrics (see Table 4 and Methods for details) and is shown in 1 cell in the heat map (e.g., the MS for E. coli and Trinity [10] is 13.61). For each data set, an assembler's MS is the sum of (0,1)-normalized scores of every single metric. The hierarchical clustering of the metric scores divides the assembly tools into 2 groups of generally high-ranked (upper half) and low-ranked (bottom half) tools. Except for Trans-ABySS [9], the MS reached for the largest human RNA-Seq data set is generally lower. Numbers in brackets next to the assembler names present the summarized metric scores (overall metric score, OMS) for all 9 data sets (see Methods). For the 3 similar human data sets infected with EBOV (Fig. 1), we added the mean MS value to the OMS. Details about the metric results for the human data set (no infection) can be found in Table 2 and for all other data sets Electronic Supplement Table S10.