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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

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