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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
  1. 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