RT Journal Article
SR Electronic
T1 Assembling metagenomes, one community at a time
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 120154
DO 10.1101/120154
A1 Andries J. van der Walt
A1 Marc W. Van Goethem
A1 Jean-Baptiste Ramond
A1 Thulani P. Makhalanyane
A1 Oleg Reva
A1 Don A. Cowan
YR 2017
UL http://biorxiv.org/content/early/2017/06/06/120154.abstract
AB 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.