GUNC: detection of chimerism and contamination in prokaryotic genomes

Genome Biology

Daniel R. Mende¹  Damian Szklarczyk²  Luis Pedro Coelho³  Thomas S. B. Schmidt⁴  Askarbek Orakov⁴  Supriya Khedkar⁴  Anthony Fullam⁴  Peer Bork⁵ 

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

关键词: Genome quality;    Genome contamination;    Metagenomics;    Metagenome-assembled genomes;    Bioinformatics;   

DOI  :  10.1186/s13059-021-02393-0

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY