metaFlye: scalable long-read metagenome assembly using repeat graphs

Abstract

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..

Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes

“…Though not explored in the present work, parameter settings can influence results and should be adjusted depending on the specific research objectives and questions. Nanopore reads were assembled using Canu (v 1.8) 23 and metaFlye (v2.6) 24 . MetaFlye was run using predicted genome sizes of 10 mb, 1 gb, and 10 gb, but was found to produce similar results (not shown), a genome size of 1 gb was chosen.…”

WeFaceNano: a user-friendly pipeline for complete ONT sequence assembly and detection of antibiotic resistance in multi-plasmid bacterial isolates

“…The Flye (v2.4.2, [ 25 , 26 ]) assembler automatically selects an optimal k-mer size based on an estimated genome size and has a default- (Flye) a meta- (metaFlye) and a plasmid- (plasmidFlye) option for assembly. Besides the default settings of Flye, metaFlye applies an algorithm that tries to generate longer contigs in order to assemble a complete genome, whereas plasmidFlye also includes smaller contigs (excluded in the metaFlye) in the assembly.…”

Surveillance of potential pathogens and antibiotic resistance in wastewater and surface water from Boston, USA and Vellore, India using long-read metagenomic sequencing

“…OPERA-MS 50 and HybridSPAdes 51 ), but in a preliminary analysis of our data, OPERA-MS produced contigs on average shorter or similar in length to our unassembled long reads (data not shown). Previous literature evaluating assemblers on mock communities has demonstrated that metaFlye, the assembler used in this work, performed well and was able to produce highly contiguous genomes 33,45 . It is important to consider that assembler performance varies by coverage and complexity of microbial communities.…”

“…Nanopore is a relatively new technology and accordingly there are few assembly pipelines available that have been rigorously evaluated 33,[44][45][46][47] . Recently, there has also been emphasis on the potential utility of short reads to improve long-read assemblies through polishing 34 ).…”