Helmholtz Gemeinschaft

Search
Browse
Statistics
Feeds

GUNC: detection of chimerism and contamination in prokaryotic genomes

[thumbnail of Original Article]
Preview
PDF (Original Article) - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
1MB
[thumbnail of Supplementary Information]
Preview
PDF (Supplementary Information) - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
1MB

Item Type:Article
Title:GUNC: detection of chimerism and contamination in prokaryotic genomes
Creators Name:Orakov, A., Fullam, A., Coelho, L.P., Khedkar, S., Szklarczyk, D., Mende, D.R., Schmidt, T.S.B. and Bork, P.
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.
Keywords:Genome Quality, Genome Contamination, Metagenomics, Metagenome-Assembled Genomes, Bioinformatics
Source:Genome Biology
ISSN:1474-760X
Publisher:BioMed Central
Volume:22
Number:1
Page Range:178
Date:13 June 2021
Official Publication:https://doi.org/10.1186/s13059-021-02393-0
PubMed:View item in PubMed

Repository Staff Only: item control page

Downloads

Downloads per month over past year

Open Access
MDC Library