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Item Type: | Preprint | ||||
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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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