Bertrand, D., Shaw, J., Kalathiyappan, M. et al. Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes. Nat Biotechnol 37, 937–944 (2019). https://doi.org/10.1038/s41587-019-0191-2
Abstract:
Characterization of microbiomes has been enabled by high-throughput metagenomic sequencing. However, existing methods are not designed to combine reads from short- and long-read technologies. We present a hybrid metagenomic assembler named OPERA-MS that integrates assembly-based metagenome clustering with repeat-aware, exact scaffolding to accurately assemble complex communities. Evaluation using defined in vitro and virtual gut microbiomes revealed that OPERA-MS assembles metagenomes with greater base pair accuracy than long-read (>5×; Canu), higher contiguity than short-read (~10× NGA50; MEGAHIT, IDBA-UD, metaSPAdes) and fewer assembly errors than non-metagenomic hybrid assemblers (2×; hybridSPAdes). OPERA-MS provides strain-resolved assembly in the presence of multiple genomes of the same species, high-quality reference genomes for rare species (
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Funding Info:
This work was supported by funding from the National Healthcare Group (NHG-CSCS/12008 and SIDI/2013/008) to K.M. and O.T.N., BMRC IAF (IAF311018) to K.M., O.T.N. and N.N. This research project is supported by the HBMS IAF-PP Asian Skin Microbiome Programme (H18/01/a0/016) and core funding from GIS (A*STAR) Singapore to N.N.