Table 1. Assembly statistics pre- and post-CD-HIT-EST.
| TAIR10 transcripts | Model Assembly (MA) |
Trinity | Trans-ABySS | Oases | SOAP denovo-Trans |
Tophat1-Cufflinks | Genome guided Trinity |
|
|---|---|---|---|---|---|---|---|---|
| Pre CD-HIT-EST | ||||||||
| Total transcripts or fragments | 15532 | 70382 | 45978 | 65594 | 52533 | 39533 | 8671 | 46064 |
| Transcriptome size (nt) | 2.61E+07 | 1.67E+07 | 1.27E+07 | 6.62E+07 | 4.21E+07 | 1.02E+07 | 1.15E+07 | 1.27E+07 |
| N50 (nt) | 1952 | 720 | 684 | 1390 | 1453 | 617 | 1624 | 646 |
| N(MA)50 (nt) | 1952 | 720 | 264 | 2802 | 2519 | 114 | 1136 | 254 |
| Median transcript/fragment length (nt) | 1456 | 85 | 115 | 804 | 523 | 103 | 1124 | 121 |
| Min. transcript/fragment length (nt) | 201 | 76 | 76 | 76 | 76 | 76 | 76 | 76 |
| Max. transcript/fragment length (nt) | 14623 | 10501 | 6888 | 7326 | 8128 | 6300 | 10502 | 7833 |
| Post CD-HIT-EST | ||||||||
| Total transcripts or fragments | 14615 | 62528 | 45281 | 16060 | 28051 | 39471 | 8395 | 42968 |
| Transcriptome size (nt) | 2.45E+07 | 1.56E+07 | 1.21E+07 | 1.15E+07 | 1.85E+07 | 1.02E+07 | 1.11E+07 | 1.20E+07 |
| N50 (nt) | 1951 | 788 | 627 | 1194 | 1485 | 617 | 1621 | 661 |
| N(MA)50 (nt) | 1951 | 788 | 260 | 798 | 1680 | 155 | 1197 | 273 |
| Median transcript/fragment length (nt) | 1451 | 87 | 113 | 477 | 216 | 103 | 1121 | 120 |
| Min. transcript/fragment length (nt) | 201 | 76 | 76 | 76 | 76 | 76 | 76 | 76 |
| Max. transcript/fragment length (nt) | 14623 | 10501 | 6888 | 7326 | 8128 | 6300 | 10502 | 7833 |