Table 2.
CRAQ metrics and quality statistics for the Drosophila melanogaster F1 individual and Solanum pennellii genome assemblies
| Assembler | N50 | BUSCO (%) | LAI | QV | CRAQ | ||||
|---|---|---|---|---|---|---|---|---|---|
| #CRH | #CSH | #CRE (R-AQI) | #CSE (S-AQI) | ||||||
| D. melanogaster (~150 Mb) | |||||||||
| Peregrine | 12.7 | 99.1 | – | 31.3 | 14.2 | 0.27 | 1.31 (87.7) | 0.047 (95.4) | |
| Canu | 13.7 | 99.5 | – | 43.5 | 12.0 | 0.24 | 0.80 (92.3) | 0.053 (94.8) | |
| HiCanu | 16.3 | 99.5 | – | 49.3 | 15.1 | 0.21 | 0.71 (93.1) | 0.084 (91.9) | |
| Hifiasm | 24.6 | 99.3 | – | 37.8 | 13.8 | 0.25 | 0.66 (93.6) | 0.043 (95.7) | |
| S. pennellii (~950 Mb) | |||||||||
| Canu- SMARTdenovo | 2.52 | 98.7 | 8.7 | 26.1 | 2.78 | 0.04 | 5.75 (56.3) | 0.119 (88.7) | |
| Canu | 1.55 | 98.6 | 7.6 | 24.3 | 3.17 | 0.07 | 9.40 (39.0) | 0.134 (87.4) | |
| SMARTdenovo | 1.06 | 98.5 | 7.4 | 22.8 | 3.21 | 0.05 | 10.98 (33.3) | 0.089 (91.5) | |
N50 lengths are in mega-bases. “–” represents values that could not be calculated because LAI can only be calculated when the intact and total LTR-RTs contribute at least 0.1% and 5%, respectively, to the genome size. Consensus quality scores (QV) were computed by Merqury. “#CRE/CSE” and “#CRH/CSH” refer to the normalized counts of CRE/CSEs and CRH/CSHs per Mbp.