Table 5.
Quality assessment of assemblies by Detonate and Transrate.
| Assembly | RSEM_EVAL scorea | SUGIT transcripts |
Contigs with positive impact scored | %Contigs with positive impact score | |
|---|---|---|---|---|---|
| CRBB hitsb | N refs with CRBBc | ||||
| Trinity-assembly | -15,240,221,881 | 229,152 | 44,765 | 274,889 | 63.74 |
| CLC-assembly | -14,103,274,074 | 257,035 | 59,991 | 384,245 | 75.60 |
| OASES-assembly | -19,974,094,466 | 376,082 | 61,612 | 459,890 | 57.61 |
| SOAP-assembly | -14,863,304,548 | 182,813 | 54,837 | 273,789 | 94.51 |
| CD-HIT-clustered | -14,369,832,453 | 465,467 | 68,603 | 511,561 | 56.43 |
| Oases-clustered | -16,058,124,749 | 655,184 | 70,611 | 549,043 | 39.69 |
| CAP3-assembled | -14,615,684,149 | 436,219 | 67,299 | 464,628 | 55.36 |
| SoGI database | -20,480,838,298 | 85,621 | 41,261 | 75,426 | 62.16 |
| Unigene set | -18,324,896,664 | 28,403 | 23,193 | 59,130 | 81.82 |
a
The higher the score, the better the assembly.
b
Number of contigs in assembly with a Conditional Reciprocal Best BLAST (CRBB) hit with the SUGIT database.
c
Number of sequences in the SUGIT database with a CRBB hit.
d
Contig with a positive RSEM_EVAL impact score.