GUNC: detection of chimerism and contamination in prokaryotic genomes

Askarbek Orakov; Anthony Fullam; Luis Pedro Coelho; Supriya Khedkar; Damian Szklarczyk; Daniel R Mende; Thomas S B Schmidt; Peer Bork

doi:10.1186/s13059-021-02393-0

GUNC: detection of chimerism and contamination in prokaryotic genomes

Genome Biol. 2021 Jun 13;22(1):178. doi: 10.1186/s13059-021-02393-0.

Authors

Askarbek Orakov^#¹, Anthony Fullam^#¹, Luis Pedro Coelho^{2

3}, Supriya Khedkar¹, Damian Szklarczyk^{4

5}, Daniel R Mende⁶, Thomas S B Schmidt⁷, Peer Bork^{8

9

10

11}

Affiliations

¹ Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
² Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
³ Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China.
⁴ Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
⁵ Swiss Institute of Bioinformatics, Lausanne, Switzerland.
⁶ Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, The Netherlands.
⁷ Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany. [email protected].
⁸ Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany. [email protected].
⁹ Max Delbrück Centre for Molecular Medicine, Berlin, Germany. [email protected].
¹⁰ Yonsei Frontier Lab (YFL), Yonsei University, Seoul, 03722, South Korea. [email protected].
¹¹ Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany. [email protected].

^# Contributed equally.

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.

Keywords: Bioinformatics; Genome contamination; Genome quality; Metagenome-assembled genomes; Metagenomics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chimerism*
Computational Biology / methods*
Contig Mapping
Genome, Bacterial*
Metagenome*
Metagenomics / methods
Phylogeny
Prokaryotic Cells / cytology
Prokaryotic Cells / metabolism
Proteobacteria / genetics*
Software*