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bioRxiv · 10.1101/2020.12.16.422776

GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes

Orakov, A. N.·Fullam, A. N.·Coelho, L. P.·Khedkar, S.·Szklarczyk, D.·Mende, D. R.·Schmidt, T. S.·Bork, P.
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Abstract

Genomes are critical units in microbiology, yet ascertaining quality in prokaryotic genomes 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 genomes 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. Source code (GPLv3+): https://github.com/grp-bork/gunc

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Orakov, A. N., Fullam, A. N., Coelho, L. P., Khedkar, S., Szklarczyk, D., Mende, D. R., Schmidt, T. S., Bork, P.. 2020-12-16. GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes. https://doi.org/10.1101/2020.12.16.422776

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