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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

MetricsGenomeQCQUAST-LGREAPR
Reference-free standard metrics (with just the genome assembly as input)YesYesYes
Metric based on gene space completeness (BUSCO)YesYesNo
BUSCO datasets and training optionsBUSCO profile datasets: 34, Augustus species: allBUSCO profile datasets: 3 (Fungal, Eukaryote, bacterial), Augustus species: 1 (fly)No
Metrics based on whole genome alignment to reference genome assemblyNoYesNo
Metrics based on mapping raw reads to the assemblyNoYesYes
Metrics based on repeat space completeness (LAI)YesNoNo
Vector contamination checkYesNoNo
Assessment of gene structure annotations setYesNoNo
Web server for the programYesNoNo
Dockerfile availabilityYesNoNo
Runtime (CPU hours)~ 1116~ 2340~ 2556