GUNC: detection of chimerism and contamination in prokaryotic genomes

Genomes are critical units in microbiology, yet ascertaining quality in prokaryotic genome assemblies remains a formidable challenge. We present GUNC (the Genome UNClutterer), a tool that accurately detects and quantifies genome chimerism based on the lineage homogeneity of individual contigs using a genome's full complement of genes. GUNC complements existing approaches by targeting previously underdetected types of contamination: we conservatively estimate that 5.7% of genomes in GenBank, 5.2% in RefSeq, and 15-30% of pre-filtered high-quality metagenome-assembled genomes in recent studies are undetected chimeras. GUNC provides a fast and robust tool to substantially improve prokaryotic genome quality.

Automated summary

GUNC is a tool that accurately detects and quantifies genome chimerism based on lineage homogeneity of individual contigs, providing a fast and robust way to improve prokaryotic genome quality. It targets previously underdetected types of contamination and can substantially enhance genome quality.