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:https://doi.org/10.1186/s13059-021-02393-0

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

Research output: Contribution to journal › Article › Academic › peer-review

74 Citations (Scopus)

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.

Original language	English
Article number	178
Journal	Genome Biology
Volume	22
Issue number	1
DOIs	https://doi.org/10.1186/s13059-021-02393-0
Publication status	Published - 1 Dec 2021
Externally published	Yes

Keywords

Bioinformatics
Genome contamination
Genome quality
Metagenome-assembled genomes
Metagenomics

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Cite this

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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{\textquoteright}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.",

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note = "Funding Information: This work was partially supported by EMBL, the German Federal Ministry of Education and Research (grant numbers: 031L0181A; 01Kl1706), the Novo Nordisk Foundation (grant number NNF15OC0016692), the H2020 European Research Council (ERC-AdG-669830), and the German Network for Bioinformatics Infrastructure (de.NBI #031A537B). Open Access funding enabled and organized by Projekt DEAL. Publisher Copyright: {\textcopyright} 2021, The Author(s).",

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AU - Fullam, Anthony

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AU - Khedkar, Supriya

AU - Szklarczyk, Damian

AU - Mende, Daniel R.

AU - Schmidt, Thomas S. B.

AU - Bork, Peer

N1 - Funding Information: This work was partially supported by EMBL, the German Federal Ministry of Education and Research (grant numbers: 031L0181A; 01Kl1706), the Novo Nordisk Foundation (grant number NNF15OC0016692), the H2020 European Research Council (ERC-AdG-669830), and the German Network for Bioinformatics Infrastructure (de.NBI #031A537B). Open Access funding enabled and organized by Projekt DEAL. Publisher Copyright: © 2021, The Author(s).

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N2 - 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.

AB - 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.

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KW - Metagenomics

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GUNC: detection of chimerism and contamination in prokaryotic genomes

Abstract

Keywords

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