Table 2. Comparison of different short read assemblers and strategies employed on the basis of various assembly parameters.
| Intial input reads |
Redundant short reads (86 million)
|
Non-redundant short reads (24 million)
|
|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Short Read Assembler | Velvet | Oases | ABySS | SOAP | CLC | Trinity | Velvet | Oases | ABySS | SOAP | CLC | Trinity | |
| Assembly Parameters | Best k-mer | (K=71) | (K=31) | (K=55) | (K=71) | Default | Default | (K=71) | (K=31) | (K=49) | (K=71) | Default | Default |
| Total number of Unigenes | 77022 | 62804 | 102826 | 97306 | 279673 | 240723 | 72302 | 55238 | 139923 | 83813 | 283777 | 234329 | |
| Maximum read length | 3293 | 8567 | 6650 | 3548 | 7070 | 14182 | 4182 | 8849 | 5001 | 3793 | 6257 | 9473 | |
| Average read length | 378 | 733 | 698 | 330 | 310 | 548 | 403 | 794 | 335 | 368 | 300 | 460 | |
| N50 read length | 454 | 1314 | 1144 | 429 | 486 | 1284 | 485 | 1378 | 482 | 474 | 434 | 791 | |
| Total map back reads (%) | 73.79 | 68.28 | 89.21 | 76.65 | 85.77 | 90.8 | 77.69 | 72.99 | 69.42 | 81.55 | 83.41 | 90.24 | |
| Unique map back reads (%) | 71.15 | 66.95 | 41.93 | 73.2 | 84.74 | 52.27 | 75.5 | 72.16 | 68.91 | 79.01 | 82.64 | 55.95 | |
| Short Read Assembler | Additive k-mer | Velvet | Oases | ABySS | SOAP | CLC | Trinity | Velvet | Oases | ABySS | SOAP | CLC | Trinity |
| Total number of Unigenes | 347958 | 115006 | 111040 | 314576 | 279673 | 240723 | 332830 | 97691 | 167892 | 295569 | 283777 | 234329 | |
| Maximum read length | 4668 | 10607 | 7659 | 4654 | 7070 | 14182 | 4931 | 10387 | 6552 | 5384 | 6257 | 9473 | |
| Average read length | 321 | 798 | 804 | 339 | 310 | 548 | 330 | 856 | 421 | 352 | 300 | 460 | |
| N50 read length | 419 | 1504 | 1317 | 458 | 486 | 1284 | 435 | 1533 | 647 | 484 | 434 | 791 | |
| Total map back reads (%) | 93.73 | 94.89 | 94.14 | 94.07 | 85.77 | 90.8 | 94.53 | 94.77 | 94.05 | 95.05 | 83.41 | 90.24 | |
| Unique map back reads (%) | 66.1 | 46.97 | 45.27 | 69.28 | 84.74 | 52.27 | 66.17 | 48.9 | 71.54 | 70.28 | 82.64 | 55.95 | |
| Short Read Assembler | Additive + TGICL | Velvet | Oases | ABySS | SOAP | CLC | Trinity | Velvet | Oases | ABySS | SOAP | CLC | Trinity |
| Total number of Unigenes | 228750 | 101055 | 85902 | 211863 | 270245 | 212093 | 219896 | 86124 | 88297 | 202713 | 274248 | 202089 | |
| Maximum read length | 7608 | 16199 | 14243 | 11102 | 9026 | 14182 | 9030 | 17565 | 10252 | 9015 | 6257 | 9474 | |
| Average read length | 374 | 871 | 930 | 396 | 317 | 475 | 385 | 932 | 610 | 407 | 307 | 444 | |
| N50 read length | 631 | 1606 | 1539 | 690 | 513 | 1035 | 658 | 1629 | 1198 | 725 | 456 | 766 | |
| Total map back reads (%) | 93.43 | 94.79 | 94.08 | 93.69 | 85.83 | 91.66 | 94.22 | 94.76 | 93.21 | 94.77 | 83.46 | 91.03 | |
| Unique map back reads (%) | 90.07 | 50.25 | 54.11 | 90.67 | 85.15 | 67.2 | 90.7 | 52.15 | 91.03 | 91.16 | 83.07 | 70.15 | |