Table 3 Statistics of each assembly step
From: Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data
|  | AFSFASSS | AFSF + ASSS | AF + SF + AS + SS | |||
|---|---|---|---|---|---|---|
| Â | Trinity | Trans-ABySS | Trinity | Trans-ABySS | Trinity | Trans-ABySS |
After merging a | Â | Â | Â | Â | Â | Â |
No. of contigs | 227,879 | 571,835 | 297,319 | 636,921 | 379,837 | 720,131 |
Total Bases | 217,485,766 | 359,411,943 | 267,708,300 | 398,478,666 | 298,801,419 | 444,024,673 |
N50 | 1,370 | 686 | 1,243 | 683 | 1,000 | 670 |
No. of contigs in N50 | 46,815 | 178,083 | 64,054 | 199,771 | 89,338 | 228,145 |
After deduplication | Â | Â | Â | Â | Â | Â |
No. of contigs | 165,174 | 152,963 | 179,876 | 138,487 | 191,858 | 128,990 |
Total Bases | 139,479,895 | 117,699,005 | 151,369,559 | 104,950,724 | 151,376,565 | 94,829,611 |
N50 | 1,146 | 935 | 1,134 | 914 | 1,016 | 878 |
No. of contigs in N50 | 34,500 | 39,253 | 38,937 | 35,969 | 44,201 | 33,877 |
After scaffolding | Â | Â | Â | Â | Â | Â |
No. of contigs | 162,090 | 152,694 | 176,983 | 138,452 | 188,653 | 129,464 |
Total Bases | 139,459,722 | 120,117,056 | 151,354,485 | 107,614,336 | 151,363,021 | 97,866,545 |
N50 | 1,177 | 960 | 1,161 | 942 | 1,041 | 907 |
No. of contigs in N50 | 33,941 | 39,124 | 38,409 | 35,915 | 43,481 | 33,927 |
Proportion of Ns | 0.12% | 0.13% | 0.12% | 0.13% | 0.12% | 0.13% |
GC content | 47.93% | 48.69% | 48.18% | 48.76% | 48.51% | 48.81% |