Assembling metagenomes, one community at a time

Andries Johannes van der Walt, Marc Warwick van Goethem, Jean Baptiste Ramond, Thulani Peter Makhalanyane, Oleg Reva, Don Arthur Cowan

Research output: Contribution to journalArticlepeer-review

79 Scopus citations


Background: 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.
Original languageEnglish (US)
JournalBMC genomics
Issue number1
StatePublished - Jul 10 2017
Externally publishedYes

Bibliographical note

Generated from Scopus record by KAUST IRTS on 2023-10-23

ASJC Scopus subject areas

  • Genetics
  • Biotechnology


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