GUNC: detection of chimerism and contamination in prokaryotic genomes

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...

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Autores principales: Orakov, Askarbek, Fullam, Anthony, Coelho, Luis Pedro, Khedkar, Supriya, Szklarczyk, Damian, Mende, Daniel R., Schmidt, Thomas S. B., Bork, Peer
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8201837/
https://www.ncbi.nlm.nih.gov/pubmed/34120611
http://dx.doi.org/10.1186/s13059-021-02393-0
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author Orakov, Askarbek
Fullam, Anthony
Coelho, Luis Pedro
Khedkar, Supriya
Szklarczyk, Damian
Mende, Daniel R.
Schmidt, Thomas S. B.
Bork, Peer
author_facet Orakov, Askarbek
Fullam, Anthony
Coelho, Luis Pedro
Khedkar, Supriya
Szklarczyk, Damian
Mende, Daniel R.
Schmidt, Thomas S. B.
Bork, Peer
author_sort Orakov, Askarbek
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02393-0.
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spelling pubmed-82018372021-06-16 GUNC: detection of chimerism and contamination in prokaryotic genomes Orakov, Askarbek Fullam, Anthony Coelho, Luis Pedro Khedkar, Supriya Szklarczyk, Damian Mende, Daniel R. Schmidt, Thomas S. B. Bork, Peer Genome Biol Method 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02393-0. BioMed Central 2021-06-13 /pmc/articles/PMC8201837/ /pubmed/34120611 http://dx.doi.org/10.1186/s13059-021-02393-0 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Orakov, Askarbek
Fullam, Anthony
Coelho, Luis Pedro
Khedkar, Supriya
Szklarczyk, Damian
Mende, Daniel R.
Schmidt, Thomas S. B.
Bork, Peer
GUNC: detection of chimerism and contamination in prokaryotic genomes
title GUNC: detection of chimerism and contamination in prokaryotic genomes
title_full GUNC: detection of chimerism and contamination in prokaryotic genomes
title_fullStr GUNC: detection of chimerism and contamination in prokaryotic genomes
title_full_unstemmed GUNC: detection of chimerism and contamination in prokaryotic genomes
title_short GUNC: detection of chimerism and contamination in prokaryotic genomes
title_sort gunc: detection of chimerism and contamination in prokaryotic genomes
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8201837/
https://www.ncbi.nlm.nih.gov/pubmed/34120611
http://dx.doi.org/10.1186/s13059-021-02393-0
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