Table 1 Comparison of the key metrics and features of the GenomeQC tool with two other assembly evaluation tools QUAST-LG and REAPR
From: GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
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 |