April 21, 2020  |  

metaFlye: scalable long-read metagenome assembly using repeat graphs

Authors: Kolmogorov, Mikhail and Rayko, Mikhail and Yuan, Jeffrey and Polevikov, Evgeny and Pevzner, Pavel

Long-read sequencing technologies substantially improved assemblies of many isolate bacterial genomes as compared to fragmented assemblies produced with short-read technologies. However, assembling complex metagenomic datasets remains a challenge even for the state-of-the-art long-read assemblers. To address this gap, we present the metaFlye assembler and demonstrate that it generates highly contiguous and accurate metagenome assemblies. In contrast to short-read metagenomics assemblers that typically fail to reconstruct full-length 16S RNA genes, metaFlye captures many 16S RNA genes within long contigs, thus providing new opportunities for analyzing the microbial “dark matter of life”. We also demonstrate that long-read metagenome assemblers significantly improve full-length plasmid and virus reconstruction as compared to short-read assemblers and reveal many novel plasmids and viruses.

Journal: BioRxiv
DOI: 10.1101/637637
Year: 2019

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