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BUSCO: Assessing Genomic Data Quality and Beyond.

Mosè Manni^1,2, Matthew R Berkeley^1,2, Mathieu Seppey^1,2

¹Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.

Current Protocols

|December 22, 2021

Summary

This summary is machine-generated.

BUSCO assesses genomic data quality using expected gene content, providing biologically meaningful metrics for genome assemblies and gene sets. This tool is crucial for ensuring data reliability in genomic analyses across diverse species.

Keywords:

gene content completeness genomes phylogenomics quality assessment single-copy orthologs

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Area of Science:

Genomics and Bioinformatics
Computational Biology
Molecular Biology

Background:

Evaluating the quality of genomic data products (e.g., genome assemblies, gene sets) is critical for identifying and correcting errors.
Accurate interpretation of genomic analyses relies on understanding the quality and reliability of input data.
Existing quality metrics, such as contiguity measures, can be complemented by biologically meaningful assessments.

Purpose of the Study:

To describe the use of the BUSCO (Benchmarking Universal Single-Copy Orthologs) tool suite for assessing genomic data quality.
To detail the application of BUSCO across various data types, including genome assemblies, transcriptomes, gene sets, and metagenome-assembled genomes.
To present novel workflows and features in BUSCO versions 4 and 5 for enhanced genomic data evaluation.

Main Methods:

Utilizing near universal single-copy orthologs from OrthoDB to estimate completeness and redundancy of genomic data.
Employing BUSCO's biologically meaningful metrics based on expected gene content to complement technical metrics.
Describing various BUSCO running modes, including batch analysis, auto-lineage workflow, and specific workflows for eukaryotic genomes.

Main Results:

BUSCO provides biologically meaningful metrics for assessing genomic data quality, complementing contiguity measures.
The tool is capable of assessing diverse sequence types from both eukaryotic and prokaryotic species.
New workflows in BUSCO v4 and v5 enhance batch analysis, automatic dataset selection, and large genome evaluation.

Conclusions:

BUSCO is an essential tool for evaluating the quality and reliability of various genomic data products.
Its ability to assess diverse data types and species makes it a versatile resource for the genomics community.
BUSCO facilitates accurate interpretation of downstream analyses by providing robust quality assessments.