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GUNC: detection of chimerism and contamination in prokaryotic genomes

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Item Type:Preprint
Title:GUNC: detection of chimerism and contamination in prokaryotic genomes
Creators Name:Orakov, A. and Fullam, A. and Coelho, L.P. and Khedkar, S. and Szklarczyk, D. and Mende, D.R. and Schmidt, T.S.B. and Bork, P.
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 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. Source code (GPLv3+): https://github.com/grp-bork/gunc
Source:bioRxiv
Publisher:Cold Spring Harbor Laboratory Press
Article Number:2020.12.16.422776
Date:16 December 2020
Official Publication:https://doi.org/10.1101/2020.12.16.422776
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https://edoc.mdc-berlin.de/20358/Final version

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