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Table 3 Comparison between Trinity and rnaSPAdes on short-read data, and hybrid assembly performed by rnaSPAdes using raw long reads and long reads corrected with Racon and RNA-Bloom for Human siNT_48 dataset

From: Extending rnaSPAdes functionality for hybrid transcriptome assembly

Assembly Trinity rnaSPAdes rnaSPAdes Hybrid rnaSPAdes + Racon rnaSPAdes + RNA-Bloom
Transcripts 463K 426K 444K 436K 443K
Misassemblies 2625 1978 2657 2389 2661
Mismatches per contig 1.78 1.32 1.43 1.39 1.43
Database coverage 0.29 0.25 0.26 0.26 0.26
Duplication ratio 2.43 1.49 2.08 1.88 2.07
50%-assembled genes 15681 15573 15570 15549 15573
95%-assembled genes 7516 7831 8186 8117 8179
50%-assembled isoforms 29150 24411 25660 24965 25669
95%-assembled isoforms 9817 9300 10038 9886 10023
  1. Best value in each row is highlighted with bold