metaFlye: scalable long-read metagenome assembly using repeat graphs

By Mikhail Kolmogorov, Derek M. Bickhart, Bahar Behsaz, Alexey A. Gurevich, M. Rayko, S. B. Shin, Kristen L Kuhn, Jeffrey Yuan, Evgeny Polevikov, T.P.L. Smith and 1 more. Nature Methods, 2020

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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. Long-read metagenomics offers a valuable approach for profiling bacterial communities. This work presents a long-read assembler, metaFlye, that specifically addresses the challenges of assembling metagenomes.

Subfields: Ecology, Molecular Biology, Pharmacology

View Paper: https://www.semanticscholar.org/paper/de4e844156c4845a2d559de6ea9ace25dff20c67