GUNC: detection of chimerism and contamination in prokaryotic genomes
Askarbek Orakov, Anthony Fullam, Luís Pedro Coelho, Supriya Khedkar, Damian Szklarczyk, Daniel R. Mende, Thomas Schmidt, Peer Bork
Abstract
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.