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首页> 外文期刊>BMC Genomics >MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples
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MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples

机译：MICOP：微生物群落分析方法，用于检测偏见样品中的病毒和真菌生物

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High throughput sequencing has spurred the development of metagenomics, which involves the direct analysis of microbial communities in various environments such as soil, ocean water, and the human body. Many existing methods based on marker genes or k-mers have limited sensitivity or are too computationally demanding for many users. Additionally, most work in metagenomics has focused on bacteria and archaea, neglecting to study other key microbes such as viruses and eukaryotes. Here we present a method, MiCoP (Microbiome Community Profiling), that uses fast-mapping of reads to build a comprehensive reference database of full genomes from viruses and eukaryotes to achieve maximum read usage and enable the analysis of the virome and eukaryome in each sample. We demonstrate that mapping of metagenomic reads is feasible for the smaller viral and eukaryotic reference databases. We show that our method is accurate on simulated and mock community data and identifies many more viral and fungal species than previously-reported results on real data from the Human Microbiome Project. MiCoP is a mapping-based method that proves more effective than existing methods at abundance profiling of viruses and eukaryotes in metagenomic samples. MiCoP can be used to detect the full diversity of these communities. The code, data, and documentation are publicly available on GitHub at: https://github.com/smangul1/MiCoP .
机译：高通量测序刺激了偏心神经的发展，涉及在各种环境中的微生物社区的直接分析，如土壤，海洋水和人体。基于标记基因或K-MERS的许多现有方法具有有限的灵敏度，或者对许多用户来说太需要苛刻。此外，Metagenomics的大多数工作都集中在细菌和古亚亚洲，忽视研究其他关键微生物，如病毒和真核生物。在这里，我们提出了一种方法，MICOP（微生物组社区分析），它使用读取的快速映射来构建来自病毒和真核生物的全基因组的综合参考数据库，以实现最大读取使用，并在每个样本中分析病毒体和真核的分析。我们证明了较小的病毒和真核参考数据库是可行的肉桂组科的映射。我们表明，我们的方法是准确的模拟和模拟群落数据，并识别了比以前报道的来自人类微生物组项目的真实数据的结果更多的病毒和真菌物种。 MICOP是一种基于映射的方法，其据现有的方法比现有方法更有效，在雌噬菌体样品中的病毒和真核生物中的丰富分析。 MICOP可用于检测这些社区的全部多样性。代码，数据和文档在github上公开可用：https://github.com/smangul1/micop。

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