Table 3 Comparison of reference-free assembly statistics for real metagenomic datasets generated in the HMP project
From: MetaCarvel: linking assembly graph motifs to biological variants
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 |