Parameters | CLC | SOAPdenovo-Trans | Trinity | Merged assembly (SOAPdenovo-Trans) | Merged assembly (CLC) |
---|---|---|---|---|---|
Number of contigs | 83,390 | 85,091 | 144,103 | 93,865 | 90,632 |
Average transcript length (bp) | 787 | 695 | 1139 | 885 | 945 |
Minimum transcript length (bp) | 300 | 300 | 300 | 300 | 300 |
Maximum transcript length (bp) | 12,370 | 12,097 | 13,939 | 13,329 | 12,167 |
N50 (bp) | 909 | 788 | 1679 | 1300 | 1450 |
N90 (bp) | 392 | 361 | 489 | 397 | 425 |
Percentage of contig ≥1 kb | 20.92 | 16.47 | 41.44 | 30% | 33.83% |
Percentage of mapped back reads to assembly | 88.51 | 83.81 | 97.49 | 93.54 | 96.98 |
Percentage of mapped reads in pairs | 78.23 | 70.71 | 89.93 | 83.67 | 87.76 |
Percentage of mapped broken paired reads | 10.28 | 13.1 | 7.86 | 9.54 | 9.22 |
Percentage of complete cores proteins by CEGMA analysis | 79.03 | 69.35 | 97.98 | 95.16 | 94.35 |
Percentage of partial cores proteins by CEGMA analysis | 93.15 | 93.15 | 99.6 | 97.74 | 98.79 |
The number of unique proteins found in blastx | 20,782 | 20,872 | 25,065 | 20,789 | 20,911 |
The number of unique contigs hit by proteins in the tblastn | 44,479 | 44,503 | 44,807 | 44,302 | 44,803 |
The number of unique contigs with reciprocal best hits | 13,730 | 13,724 | 15,690 | 14,003 | 14,101 |
The number of unique contigs with orthologue hit ratio of 0.8–1 | 5963 | 7249 | 12,903 | 7750 | 8423 |
RSEM-EVAL score | −19,590,755,435 | −22,457,309,826 | −11,702,493,371 | −14,998,853,445 | −13,665,328,361 |