Long-read sequencing technologies have substantially improved the assemblies of many isolate bacterial genomes as compared to fragmented short-read assemblies. However, assembling complex metagenomic datasets remains difficult even for state-of-the-art long-read assemblers. Here we present metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. First, we benchmarked metaFlye using simulated and mock bacterial communities and show that it consistently produces assemblies with better completeness and contiguity than state-of-the-art long-read assemblers. Second, we performed long-read sequencing of the sheep microbiome and applied metaFlye to reconstruct 63 complete or nearly complete bacterial genomes within single contigs. Finally, we show that long-read assembly of human microbiomes enables the discovery of full-length biosynthetic gene clusters that encode biomedically important natural products.

与片段化的短读组装相比，长读测序技术已大大改善了许多分离细菌基因组的组装。但是，即使对于最先进的长读取汇编器，仍然难以汇编复杂的宏基因组数据集。在这里，我们介绍了metaFlye，它解决了重要的长期宏基因组学难题，例如细菌组成不均和种内异质性。首先，我们使用模拟细菌和模拟细菌群落对metaFlye进行了基准测试，结果表明与传统的长时间阅读的汇编程序相比，它始终可以产生具有更好完整性和邻接性的汇编程序。其次，我们对绵羊微生物组进行了长时间阅读测序，并应用metaFlye在单个重叠群内重建了63个完整或接近完整的细菌基因组。最后，