Table 3.
Comparison of reference-free assembly statistics for real metagenomic datasets generated in the HMP project
| Dataset | Method | #Scaffolds | Assembly size (Mbp) | #Scaffolds > 50 kbp | Largest scaffold (kbp) | #Concordant mate pairs | Length at 1 Mbp (kbp) | Length at 10 Mbp (kbp) | Length at 50 Mbp (kbp) |
|---|---|---|---|---|---|---|---|---|---|
| SRS049959 | OPERA-LG | 198,206 | 273.2 | 473 | 530.1 | 97,428,296 (82.1%) | 258.6 | 126.3 | 38.9 |
| MetaCarvel | 108,437 | 277.0 | 487 | 518.2 | 98,107,950 (85.5%) | 356.7 | 154.1 | 39.5 | |
| metaSPAdes | 98,318 | 268.3 | 489 | 476.5 | 91,870,816 (80.0%) | 422.8 | 164.1 | 44.8 | |
| OPERA-LG (M) | 97,486 | 267.7 | 518 | 476.5 | 91,948,044 (80.1%) | 405.1 | 162.2 | 47.0 | |
| MetaCarvel (M) | 98,073 | 268.1 | 492 | 868.8 | 92,183,496 (80.3%) | 749.8 | 211.0 | 49.2 | |
| SRS020233 | OPERA-LG | 128,250 | 279.8 | 393 | 381.6 | 91,464,778 (84.9%) | 286.5 | 139.7 | 35.4 |
| MetaCarvel | 141,438 | 282.5 | 421 | 430.2 | 92,077,670 (86.9%) | 368.6 | 154.3 | 37.8 | |
| metaSPAdes | 122,613 | 279.6 | 437 | 573.8 | 91,577,014 (85.9%) | 351.9 | 163.9 | 40.9 | |
| OPERA-LG (M) | 122,143 | 279.9 | 459 | 573.8 | 91,622,740 (85.3%) | 372.1 | 158.3 | 42.4 | |
| MetaCarvel (M) | 122,776 | 280.8 | 471 | 587.2 | 91,840,800 (85.3%) | 584.7 | 187.1 | 44.7 | |
| SRR2241511 | OPERA-LG | 631 | 284.4 | 5 | 962.9 | 12,618,990 (83.9%) | 19.3 | NA | NA |
| MetaCarvel | 533 | 285.9 | 6 | 126.1 | 12,665,752 (84.2%) | 27.7 | NA | NA | |
| metaSPAdes | 774 | 334.5 | 4 | 570.3 | 13,838,686 (91.0%) | 20.6 | NA | NA | |
| OPERA-LG (M) | 733 | 334.3 | 6 | 124.9 | 12,875,136 (85.6%) | 20.9 | NA | NA | |
| MetaCarvel (M) | 652 | 335.4 | 11 | 126.3 | 12,910,216 (85.9%) | 37.74 | NA | NA | |
| SRR2241598 | OPERA-LG | 60,601 | 117.6 | 75 | 217.4 | 19,423,228 (51.6%) | 148.3 | 35.1 | 4.1 |
| MetaCarvel | 56,503 | 119.1 | 100 | 319.2 | 20,047,708 (54.0%) | 184.2 | 46.6 | 5.7 | |
| metaSPAdes | 48,403 | 113.6 | 102 | 417.4 | 16,771,928 (45.2%) | 206.9 | 46.5 | 6.2 | |
| OPERA-LG (M) | 43,908 | 109.4 | 105 | 282.9 | 16,749,600 (45.1%) | 206.9 | 47.9 | 6.6 | |
| MetaCarvel (M) | 42,927 | 110.2 | 190 | 417.4 | 16,893,882 (45.5%) | 336.43 | 97.5 | 8.7 |
For the concordant mate pairs, the number in the parenthesis denotes the percentage of total read pairs mapped concordantly to scaffolds. In methods, (M) denotes scaffolds generated using metaSPAdes contigs as input to MetaCarvel and OPERA-LG