Table 4 Effect of concatenating assemblies on CDS length
Illumina derived datasets | Simulated datasets | ||||||||
|---|---|---|---|---|---|---|---|---|---|
Assembler | L. stagnalis | S. cerevisiae | Caenorhabditis sp. | D. simulans | H. rhamnoides | N. benthamiaana | D. melanogaster | C.elegans | |
Number of extended CDSsa | CLC | 8,195 (38%) | 1,333 (23%) | 7,255 (44%) | 5,490 (34%) | 11,508 (38%) | 24,218 (47%) | 1,888 (23%) | 1,534 (13%) |
IDBA_tran | 13,401 (27%) | 957 (16%) | 11,717 (38%) | 7,586 (25%) | 11,427 (24%) | 48,830 (36%) | 1,960 (23%) | 2,054 (18%) | |
Trinity | 23,532 (34%) | 2,879 (27%) | 28,918 (44%) | 11,638 (33%) | 21,032 (35%) | 78,038 (40%) | 7,817 (38%) | 5,808 (33%) | |
Cumulated extended CDS length (bp) | CLC | 9,289,434 | 913,872 | 6,758,496 | 5,921,460 | 6,816,978 | 23,238,501 | 2,662,092 | 1,107,756 |
IDBA_tran | 23,112,789 | 121,116 | 9,431,703 | 5,795,478 | 5,143,413 | 36,408,087 | 2,311,569 | 1,433,037 | |
Trinity | 33,055,113 | 2,749,041 | 30,317,865 | 14,029,893 | 16,390,158 | 53,633,142 | 10,201,314 | 4,291,554 | |
Mean extended CDS length (bp) | CLC | 1,134 | 686 | 932 | 1,079 | 592 | 960 | 1,410 | 722 |
IDBA_tran | 1,725 | 127 | 805 | 764 | 450 | 746 | 1,179 | 698 | |
Trinity | 1,405 | 955 | 1,048 | 1,206 | 779 | 687 | 1,305 | 739 | |