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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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Detalles Bibliográficos
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:
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
Descripción
Sumario: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.