Skip to main content

Table 4 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 GM12878 dataset

From: Extending rnaSPAdes functionality for hybrid transcriptome assembly

Assembly Trinity rnaSPAdes rnaSPAdes Hybrid rnaSPAdes + Racon rnaSPAdes + RNA-Bloom
Transcripts 278K 234K 237K 237K 243K
Misassemblies 2548 2247 2350 2332 2763
Mismatches per contig 1.93 1.66 1.69 1.69 1.76
Database coverage 0.21 0.18 0.19 0.19 0.19
Duplication ratio 1.86 1.28 1.41 1.41 1.58
50%-assembled genes 11436 11506 11544 11515 11598
95%-assembled genes 4427 5075 5264 5283 5349
50%-assembled isoforms 19396 16396 16674 16639 17489
95%-assembled isoforms 5463 5713 6038 6039 6223
  1. Best value in each row is highlighted with bold