BUSCO

BUSCO assesses genome assembly, annotated gene set, and transcriptome completeness by detecting near-universal single-copy orthologs to provide biologically meaningful completeness and redundancy metrics.

Key Features:

• Comprehensive Assessment: Evaluates genome assemblies, annotated gene sets, assembled transcriptomes, and metagenome-assembled genomes for both eukaryotes and prokaryotes.
• Biologically Meaningful Metrics: Uses near-universal single-copy ortholog datasets from OrthoDB to report completeness and redundancy by quantifying presence, absence, and fragmentation of orthologs, complementing contiguity measures such as N50.
• Flexible and Extensible Software: Implemented in Python and refactored for flexibility and extensibility, supporting batch analysis and novel workflows for high-throughput assessments.
• Automatic Lineage Workflow: Automatically selects an appropriate lineage dataset when not specified, facilitating analysis of metagenome-assembled genomes of unknown origin.
• Enhanced Data Sets: Expanded OrthoDB-derived datasets improve species sampling and resolution across vertebrates, arthropods, fungi, prokaryotes, nematodes, protists, and plants.
• Phylogenomic Applications: Produces gene sets usable for construction of phylogenomic trees and visualization of syntenies.

Scientific Applications:

• Quality Control: Assess completeness and identify missing or fragmented orthologs in genome assemblies and gene sets.
• Comparative Genomics: Compare expected gene content across species using lineage-specific single-copy ortholog sets.
• Gene Predictor Training: Inform training and evaluation of gene prediction models by indicating genome completeness and redundancy.
• Metagenomics: Assess metagenome-assembled genomes and transcriptomes derived from metagenomic datasets.
• Phylogenomics: Provide single-copy ortholog markers for phylogenomic inference and synteny analyses.

Methodology:

Compares input sequences against curated sets of near-universal single-copy orthologs (from OrthoDB) expected for a specified lineage, quantifies presence, absence, or fragmentation to produce completeness and redundancy scores, and supports manual dataset specification, automatic lineage selection, and batch processing.