Table 1.
Comparison of the key metrics and features of the GenomeQC tool with two other assembly evaluation tools QUAST-LG and REAPR
| Metrics | GenomeQC | QUAST-LG | REAPR |
|---|---|---|---|
| Reference-free standard metrics (with just the genome assembly as input) | Yes | Yes | Yes |
| Metric based on gene space completeness (BUSCO) | Yes | Yes | No |
| BUSCO datasets and training options | BUSCO profile datasets: 34, Augustus species: all | BUSCO profile datasets: 3 (Fungal, Eukaryote, bacterial), Augustus species: 1 (fly) | No |
| Metrics based on whole genome alignment to reference genome assembly | No | Yes | No |
| Metrics based on mapping raw reads to the assembly | No | Yes | Yes |
| Metrics based on repeat space completeness (LAI) | Yes | No | No |
| Vector contamination check | Yes | No | No |
| Assessment of gene structure annotations set | Yes | No | No |
| Web server for the program | Yes | No | No |
| Dockerfile availability | Yes | No | No |
| Runtime (CPU hours) | ~ 1116 | ~ 2340 | ~ 2556 |