Table 6 Statistics for HiFi assemblies at various levels of haploid genome coverage. Genome coverage of at least 25× is required to achieve a contiguous assembly. However, assemblies below 30× coverage have a large proportion of contigs with phase switches (Fig. 8)
Statistic | HiFi-Canu assemblies | |||||
|---|---|---|---|---|---|---|
Haploid genome coverage | 50× | 40× | 30× | 25× | 20× | 10× |
Assembly size | 269.0 Mb | 267.5 Mb | 258.1 Mb | 254.5 Mb | 252.3 Mb | 212.5 Mb |
# of contigs | 1,063 | 982 | 825 | 872 | 1,215 | 3,285 |
Assembly N/L50 | 28/2.4 Mb | 28/2.7 Mb | 48/1.7 Mb | 72/1.1 Mb | 139/493.9 Kb | 735/86.4 Kb |
Assembly N/L90 | 176/119.6 Kb | 162/141.0 Kb | 220/186.0 Kb | 307/153.4 Kb | 566/93.6 Kb | 2379/30.5 Kb |
Maximum contig length | 9.3 Mb | 10.6 Mb | 5.8 Mb | 5.1 Mb | 2.7 Mb | 563.8 Kb |