Table 3:
Benchmarking of BinPacker, Bridger, IDBA-tran, RNA-Bloom, rnaSPAdes, SOAPdenovo-Trans, SPAdes, Trans-ABySS, and Trinity on Human simulated RNA-Seq dataset
| Parameter | BinPacker | Bridger | IDBA | Bloom | rnaSPAdes | SOAP | SPAdes | ABySS | Trinity |
|---|---|---|---|---|---|---|---|---|---|
| Transcripts | 76,736 | 52,151 | 58,466 | 65,968 | 37,730 | 35,096 | 42,264 | 67,511 | 62,831 |
| Misassemblies | 7,919 | 3,512 | 174 | 358 | 309 | 198 | 443 | 126* | 1,554 |
| Duplication ratio | 2.19 | 1.38 | 1.01 | 1.93 | 1.26 | 1.08 | 1.00* | 1.24 | 1.74 |
| Database coverage, % | 20.9 | 18.5 | 21.4 | 24.6* | 23.2 | 19.4 | 20.5 | 23.1 | 24.4 |
| 50%-assembled genes | 11,828 | 11,476 | 13,175 | 12,869 | 14,075* | 12,610 | 13,569 | 12,740 | 13,289 |
| 95%-assembled genes | 7,320 | 6,417 | 2,729 | 8,910 | 10,934* | 7,685 | 8,526 | 7,225 | 9,049 |
| 50%-assembled isoforms | 17,415 | 15,423 | 18,181 | 21,035* | 19,531 | 15,638 | 16,437 | 19,250 | 20,965 |
| 95%-assembled isoforms | 9,091 | 7,298 | 2,744 | 12,108 | 13,387* | 8,151 | 8,638 | 7,662 | 12,301 |
The annotated transcriptome of H. sapiens GRCh37.p13 consists of 57,820 genes and 196,520 isoforms. All contigs shorter than 200 bp were filtered out prior to the analysis. The best values for each metric are indicated with asterisk.