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 |