Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany.
Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
Genome Biol. 2021 Jun 13;22(1):178. doi: 10.1186/s13059-021-02393-0.
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.
基因组是微生物学的关键单位，但确定原核生物基因组组装的质量仍然是一个艰巨的挑战。我们提出了 GUNC（基因组去芜存菁器），这是一种工具，它基于单个连续序列的谱系同质性，利用基因组的全部基因来准确检测和量化基因组嵌合体。GUNC 通过针对以前检测不到的污染类型来补充现有方法：我们保守估计，GenBank 中的 5.7%、RefSeq 中的 5.2%以及最近研究中经过预过滤的“高质量”宏基因组组装基因组中的 15-30%是未检测到的嵌合体。GUNC 提供了一种快速而强大的工具，可以大大提高原核生物基因组的质量。
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