Compleasm

Compleasm evaluates genome assembly, gene set, and transcriptome completeness by quantifying near-universal single-copy orthologs to produce evolutionarily informed completeness assessments.

Key Features:

• Assessment targets: Evaluates genome assemblies, gene sets, and transcriptomes for gene completeness.
• Ortholog-based quantification: Provides quantitative assessments based on evolutionarily informed expectations derived from near-universal single-copy orthologs.
• Method integration: Leverages the miniprot protein-to-genome aligner and conserved orthologous gene sets from BUSCO for alignment-driven detection.
• Speed: Performs assessments up to 14 times faster than BUSCO on human assemblies.
• Accuracy: Reports completeness rates of 99.6% versus BUSCO's 95.7%, aligning with annotation completeness observed for T2T-CHM13.
• Scalability: Suited for large genome assemblies and analysis of substantial numbers of datasets due to improved computational efficiency.

Scientific Applications:

• Quality assessment of genome assemblies: Quantifies gene completeness to evaluate assembly quality and inform confidence in downstream gene predictions and annotations.
• Support for downstream analyses: Identifies incomplete assemblies to prevent errors in functional annotation, comparative genomics, and evolutionary studies.

Methodology:

Leverages the miniprot protein-to-genome aligner and utilizes conserved orthologous genes from BUSCO to quantify presence of near-universal single-copy orthologs for completeness evaluation.