BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes

TL;DR

This paper introduces major updates to BUSCO, a tool for assessing genome completeness, including new workflows, broader phylogenetic coverage, and the ability to analyze metagenomes of unknown origin.

Contribution

The paper presents new functionalities and dataset expansions in BUSCO, enabling phylogenetic placement and improved efficiency for diverse genomic data types.

Findings

Enhanced phylogenetic placement for unknown genomes

Increased efficiency on large eukaryotic genomes

Broader applicability to eukaryotic, prokaryotic, and viral data

Abstract

Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. Here we present new functionalities and major improvements of the BUSCO software, as well as the renewal and expansion of the underlying datasets in sync with the OrthoDB v10 release. Among the major novelties, BUSCO now enables phylogenetic placement of the input sequence to automatically select the most appropriate dataset for the assessment, allowing the analysis of metagenome-assembled genomes of unknown origin. A newly-introduced genome workflow increases the efficiency and runtimes especially on large eukaryotic genomes. BUSCO is the only tool capable of assessing both eukaryotic and prokaryotic species, and can be applied to various data types, from genome assemblies and metagenomic bins, to transcriptomes and gene sets.