Table 3.
Assembly statistics for different assemblers using short-reads, short-reads with virtual barcodes, or short- and long-reads on mock communities
| Total assembly length | Genome fraction (%) | Largest alignment | Overall N50 | Overall N70 | Overall N90 | Overall NA50 | NA50 per strain | NGA50 per strain | Non-zero NGA50 | |
|---|---|---|---|---|---|---|---|---|---|---|
| ATCC-MSA-1003 | ||||||||||
| Pangaea-MP | 61,826,844 | 77.21 | 4,613,760 | 419,529 | 123,550 | 6,828 | 227,880 | 551,174 | 599,918 | 16 |
| MetaPlatanus | 50,420,118 | 65.78 | 4,143,574 | 232,150 | 64,539 | 2,484 | 207,981 | 342,514 | 338,045 | 12 |
| Pangaea-HS | 61,432,598 | 82.69 | 2,824,147 | 475,582 | 150,196 | 6,824 | 338,892 | 410,176 | 412,875 | 16 |
| hybridSPAdes | 60,794,505 | 82.93 | 1,518,615 | 255,665 | 88,668 | 6,333 | 236,258 | 229,866 | 229,492 | 16 |
| Pangaea-OP | 53,145,042 | 63.25 | 3,027,146 | 345,524 | 108,841 | 4,801 | 236,263 | 219,172 | 311,080 | 16 |
| OPERA-MS | 44,017,454 | 57.87 | 885,414 | 55,544 | 19,419 | 2,919 | 49,863 | 104,942 | 105,557 | 11 |
| Athena | 60,077,880 | 81.57 | 1,175,563 | 176,953 | 81,610 | 7,766 | 173,018 | 158,550 | 157,166 | 16 |
| metaSPAdes | 60,648,311 | 82.46 | 776,102 | 112,342 | 49,466 | 5,429 | 105,630 | 119,253 | 118,391 | 16 |
| CAMI-high | ||||||||||
| Pangaea-MP | 790,047,911 | 27.83 | 3,200,312 | 193,286 | 92,221 | 22,625 | 179,405 | 66,510 | 47,460 | 187 |
| MetaPlatanus | 759,582,683 | 28.28 | 2,525,754 | 146,524 | 66,065 | 11,900 | 143,981 | 55,924 | 39,696 | 187 |
| Pangaea-HS | 765,341,275 | 26.99 | 2,552,627 | 185,706 | 86,908 | 22,576 | 172,580 | 57,562 | 43,844 | 180 |
| hybridSPAdes | 759,703,702 | 27.04 | 3,195,687 | 148,522 | 68,335 | 14,950 | 140,963 | 50,524 | 39,710 | 179 |
| Pangaea-OP | 790,451,622 | 27.40 | 3,370,333 | 172,800 | 78,129 | 16,150 | 160,739 | 60,235 | 45,323 | 181 |
| OPERA-MS | 797,297,690 | 27.01 | 1,860,977 | 95,314 | 41,765 | 8,017 | 94,811 | 34,746 | 21,890 | 174 |
| Athena | 738,341,840 | 26.27 | 2,520,898 | 151,113 | 72,087 | 17,299 | 149,290 | 49,612 | 36,428 | 173 |
| metaSPAdes | 759,108,499 | 27.01 | 2,520,915 | 133,877 | 62,467 | 12,521 | 132,603 | 45,261 | 34,551 | 177 |
| ZYMO | ||||||||||
| Pangaea-MP | 36,160,031 | 48.66 | 2,719,840 | 444,651 | 181,141 | 73,012 | 345,995 | 391,840 | 392,681 | 6 |
| MetaPlatanus | 35,906,273 | 48.91 | 2,423,776 | 250,282 | 137,973 | 50,299 | 242,683 | 429,587 | 428,086 | 6 |
| Pangaea-HS | 35,806,901 | 48.47 | 2,350,555 | 444,276 | 203,542 | 76,164 | 342,859 | 697,544 | 704,255 | 6 |
| HybridSPAdes | 35,517,607 | 48.63 | 1,799,936 | 289,924 | 154,423 | 69,345 | 287,773 | 387,101 | 383,552 | 6 |
| Pangaea-OP | 35,917,521 | 48.62 | 3,579,300 | 347,153 | 156,102 | 59,828 | 301,599 | 756,021 | 757,488 | 6 |
| OPERA-MS | 35,334,818 | 48.28 | 3,579,284 | 131,207 | 70,061 | 21,837 | 124,358 | 683,735 | 681,358 | 6 |
| Athena | 34,567,225 | 47.34 | 1,282,835 | 237,784 | 126,002 | 59,781 | 232,219 | 214,809 | 210,268 | 6 |
| metaSPAdes | 35,511,020 | 48.46 | 847,644 | 191,688 | 106,796 | 44,425 | 191,688 | 183,935 | 179,371 | 6 |
Pangaea-MP stands for Pangaea-MetaPlatanus, Pangaea-HS stands for Pangaea-hybridSPAdes and Pangaea-OP stands for Pangaea-Operams.
The highest values are in bold.