Number of reconstructed protein coding genes. Number of full-length protein coding genes reconstructed by each method using inputs with different depth of coverage: D. melanogaster data sets (a), S. pombe data sets (b). Number of reconstructed genes were shown using Dme-3g (c), Dme-13g (d), Spo-1g (e) and Spo-6.8g (f) data sets, which included full-length reconstructed genes with 100% (blue) and at least 95% identity (reddish brown); partial-length reconstructed genes: 80% (green) and 50% (purple). Trinity assembly with strand specific option “--SS_lib_type RF” was marked as asterisk. The assessment of Trinity without “--jaccard_clip” option was shown as “Trinity#” using Spo-6.8g data set (f).