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Table 4 Performance comparison of different scaffolders based on varying the sequencing depth on the MBARC-26 dataset.

From: MetaCarvel: linking assembly graph motifs to biological variants

Input size (millions of reads) Metric No. of scaffolds Length at 1 Mbp (bp) Length at 10 Mbp (bp) Length at 50 Mbp (bp) CPU time Peak memory (GB)
2 OPERA-LG 29,831 988,539 90,227 719 44 s 2.2
metaSPAdes 61,592 594,287 92,217 783 NA 8.2
MetaCarvel 29,883 699,981 90,014 718 58 s 2.1
4 OPERA-LG 22,952 1,257,853 168,019 4393 2 min 16 s 2.8
metaSPAdes 49,199 1,635,634 190,132 3823 NA 10.1
MetaCarvel 23,003 1,257,853 168,390 4374 2 min 48 s 3
8 OPERA-LG 21,866 1,257,855 393,755 34,351 3 min 13 s 4
metaSPAdes 39,460 1,635,634 190,132 31,823 NA 14.3
MetaCarvel 23,003 1,223,449 423,739 32,331 3 min 47 s 3.8
10 OPERA-LG 21,413 1,257,855 402,996 50,874 8 min 01 s 5
metaSPAdes 35,754 1,635,634 478,925 52,165 NA 22.5
MetaCarvel 21,033 1,332,109 418,821 49,839 10 min 41 s 5.2
14 OPERA-LG 18,370 1,461,964 676,339 72,581 14 min 08 s 8.1
metaSPAdes 29,298 1,635,789 668,856 78,337 NA 28.1
MetaCarvel 18,281 1,463,318 686,311 73,522 13 min 14 s 7.4
  1. The runtime for metaSPAdes is not mentioned (marked NA) since we cannot separate the assembly from the scaffolding steps. Maximum contig size is the same for OPERA-LG and MetaCarvel because the same input assembly was used as input to them