Table 1.
Comparison of the assemblies produced by RAmbler, hifiasm, LJA, HiCANU, and Verkko on the HiFi reads extracted around the centromeres of human Chromosomes 8 and X, for several choices of input assemblies and HiFi reads
| Chr | Input assembly | HiFi reads | Depth | Repetitive region | # Selected reads | Selected reads sum (Mb) | Expected size (Mb) | Assembler | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Start (Mb) | End (Mb) | RAmbler | hifiasm | LJA | HiCANU | Verkko | ||||||||
| 8 | HG38 | HG002 | 67.5× | 43.5 | 46.5 | 15,620 | 249.038 | 3.689 | # Contigs | 2 | 3 | 39 | – | 66 |
| Total (bp) | 3,885,290 | 3,632,973 | 7,573,022 | 8,186,622 | ||||||||||
| Longest contig | 3,627,559 | 1,843,336 | 2,701,877 | 1,374,826 | ||||||||||
| HG00733 | 32.8× | 43.5 | 46.5 | 7241 | 99.356 | 3.029 | # Contigs | 1 | 3 | 74 | 44 | 103 | ||
| Total (bp) | 3,805,715 | 3,692,973 | 6,653,621 | 6,279,128 | 7,267,808 | |||||||||
| Longest contig | 3,805,715 | 3,483,042 | 1,384,931 | 1,002,430 | 1,710,467 | |||||||||
| HG01346 | 26× | 42.0 | 48.0 | 9579 | 177.120 | 6.812 | # Contigs | 3 | 5 | 91 | 73 | 134 | ||
| Total (bp) | 7,553,039 | 6,637,843 | 12,660,338 | 13,840,156 | 13,671,832 | |||||||||
| Longest contig | 6,229,877 | 6,213,919 | 4,017,234 | 6,043,945 | 2,981,689 | |||||||||
| T2T | CHM13 | 32.4× | 43.5 | 46.5 | 5591 | 101.370 | 3.129 | # Contigs | 1 | 1 | 1 | 10 | 1 | |
| Total (bp) | 3,040,965 | 3,040,965 | 3,040,948 | 3,343,237 | 3,032,370 | |||||||||
| Longest contig | 3,040,965 | 3,040,965 | 3,040,948 | 3,033,722 | 3,032,370 | |||||||||
| MAT002 | HG002 | 66× | 43.5 | 47.0 | 14,393 | 229.495 | 3.477 | # Contigs | 1 | 3 | 26 | – | 51 | |
| Total (bp) | 3,271,813 | 3,309,709 | 6,861,347 | 7,415,002 | ||||||||||
| Longest contig | 3,271,813 | 1,776,606 | 2,701,877 | 1,374,826 | ||||||||||
| X | HG38 | HG002 | 34.2× | 57.5 | 63.0 | 9665 | 155.687 | 4.552 | # Contigs | 1 | 1 | 1 | 1 | N/A |
| Total (bp) | 4,678,725 | 4,678,719 | 4,663,887 | 4,669,944 | ||||||||||
| Longest contig | 4,678,725 | 4,678,719 | 4,663,887 | 4,669,944 | ||||||||||
| HG00733 | 31.8× | 57.25 | 64.0 | 15,333 | 209.268 | 6.581 | # Contigs | 2 | 3 | 114 | 103 | 170 | ||
| Total (bp) | 5,653,597 | 5,279,187 | 12,115,053 | 13,853,128 | 13,649,195 | |||||||||
| Longest contig | 3,813,195 | 3,408,909 | 1,675,295 | 2,970,002 | 3,984,187 | |||||||||
| HG01346 | 25.5× | 57.25 | 64.0 | 9679 | 179.004 | 7.020 | # Contigs | 1 | 5 | 74 | 92 | 140 | ||
| Total (bp) | 7,378,373 | 7,072,503 | 12,305,066 | 14,376,243 | 13,718,592 | |||||||||
| Longest contig | 7,378,373 | 3,232,572 | 4,247,266 | 3,280,524 | 4,251,271 | |||||||||
| T2T | CHM13 | 34× | 57.5 | 62.0 | 8488 | 153.883 | 4.526 | # Contigs | 1 | 2 | 3 | 22 | 10 | |
| Total (bp) | 4,468,109 | 4,533,307 | 4,536,587 | 5,081,155 | 4,575,146 | |||||||||
| Longest contig | 4,468,109 | 4,486,438 | 4,074,724 | 2,016,666 | 1,940,381 | |||||||||
| MAT002 | HG002 | 33× | 57.5 | 62.0 | 9362 | 150.793 | 4.569 | # Contigs | 2 | 2 | 3 | – | 4 | |
| Total (bp) | 4,566,785 | 4,566,777 | 4,542,009 | 4,546,175 | ||||||||||
| Longest contig | 4,542,010 | 4,542,004 | 4,180,812 | 4,141,556 | ||||||||||
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Numbers in bold indicate the assemblies with the fewest contigs in each row.
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(–) The assembler timed out after 96 h; (N/A) the assembler finished execution but produced no output.
