Although plasmids are important for bacterial survival and adaptation, plasmid detection and assembly from genomic, let alone metagenomic, samples remain challenging. The recently developed plasmidSPAdes assembler addressed some of these challenges in the case of isolate genomes but stopped short of detecting plasmids in metagenomic assemblies, an untapped source of yet to be discovered plasmids. We present the metaplasmidSPAdes tool for plasmid assembly in metagenomic data sets that reduced the false positive rate of plasmid detection compared with the state-of-the-art approaches. We assembled plasmids in diverse data sets and have shown that thousands of plasmids remained below the radar in already completed genomic and metagenomic studies. Our analysis revealed the extreme variability of plasmids and has led to the discovery of many novel plasmids (including many plasmids carrying antibiotic-resistance genes) without significant similarities to currently known ones.

中文翻译：

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基因组和宏基因组数据集中的质粒检测和组装。

尽管质粒对于细菌存活和适应很重要，但从基因组（更不用说宏基因组学）进行质粒检测和组装了，样品仍然具有挑战性。在分离基因组的情况下，最近开发的质粒SPAdes装配体解决了其中的一些挑战，但未能检测到宏基因组装配体中的质粒，这是尚未发现的质粒的未开发来源。我们在宏基因组数据集中提供了用于质粒组装的metaplasmidSPAdes工具，与最新技术方法相比，该工具减少了质粒检测的假阳性率。我们将质粒组装在不同的数据集中，并表明在已经完成的基因组和宏基因组研究中，成千上万的质粒仍在雷达之下。