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Table 2 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 MCF7 dataset

From: Extending rnaSPAdes functionality for hybrid transcriptome assembly

Assembly Trinity rnaSPAdes rnaSPAdes hybrid rnaSPAdes + Racon rnaSPAdes + RNA-Bloom
Transcripts 305K 243K 264K 260K 270K
Misassemblies 2719 2170 3968 3001 4059
Mismatches per contig 1.85 1.50 2.31 1.82 2.26
Database coverage 0.26 0.23 0.25 0.24 0.25
Duplication ratio 2.45 1.45 2.96 2.28 2.94
50%-assembled genes 13422 13546 13990 13728 13974
95%-assembled genes 6091 6310 7379 7061 7370
50%-assembled isoforms 24575 21048 23885 22427 23795
95%-assembled isoforms 7856 7355 9333 8657 9273
  1. Since for this dataset FL reads are available, they were fed into rnaSPAdes using the appropriate option. Best value in each row is highlighted with bold