Assembling metagenomes, one community at a time

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TitleAssembling metagenomes, one community at a timeAbstractBackground: Metagenomics allows unprecedented access to uncultured environmental microorganisms. The analysis of metagenomic sequences facilitates gene prediction and annotation, and enables the assembly of draft genomes, including uncultured members of a community. However, while several platforms have been developed for this critical step, there is currently no clear framework for the assembly of metagenomic sequence data. Results: To assist with selection of an appropriate metagenome assembler we evaluated the capabilities of nine prominent assembly tools on nine publicly-available environmental metagenomes, as well as three simulated datasets. Overall, we found that SPAdes provided the largest contigs and highest N50 values across 6 of the 9 environmental datasets, followed by MEGAHIT and metaSPAdes. MEGAHIT emerged as a computationally inexpensive alternative to SPAdes, assembling the most complex dataset using less than 500 GB of RAM and within 10 hours. Conclusions: We found that assembler choice ultimately depends on the scientific question, the available resources and the bioinformatic competence of the researcher. We provide a concise workflow for the selection of the best assembly tool. Â© 2017 The Author(s).Funding DetailsUP, University of Pretoria; 102,910, NRF, National Research Foundation; 97,891, NRF, National Research Foundation

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1st Authorvan der Walt, A. Authorvan der Walt, A.van Goethem, M.Ramond, J.-B.Makhalanyane, T.Reva, O.Cowan, D.Year2017JournalBMC GenomicsVolume18Number1DOI10.1186/s12864-017-3918-9URLhttps://www.scopus.com/inward/recor.....13fb0e6290bfd673e53e07ddfPublisherBioMed Central Ltd.Keywordsbioinformaticsecologyhumanmetagenomescientistsimulationworkflowbenchmarkingenvironmentgenetic databasemetagenomicsprocedures, BenchmarkingDatabases, GeneticEnvironmentMetagenomicsAuthor KeywordsAssemblerBioinformaticsIlumina HiSeqMetagenome assemblyMicrobial ecology

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Citationvan der Walt, A., van Goethem, M., Ramond, J.-B., Makhalanyane, T., Reva, O. and Cowan, D. (2017). Assembling metagenomes, one community at a time. BMC Genomics, 18(1)