Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes
| Autor: | Kern Rei Chng, Janja Paliska Soldo, Barnaby Edward Young, Jia Yu Koh, Kalisvar Marimuthu, Niranjan Nagarajan, Denis Bertrand, James C. Shaw, Amanda Hui Qi Ng, Mile Šikić, Mirta Dvornicic, Chenhao Li, Chengxuan Tong, Oon Tek Ng, Timothy Barkham, Manesh Kalathiyappan, M. Senthil Kumar |
|---|---|
| Rok vydání: | 2019 |
| Předmět: |
Sequence analysis
Computer science Biomedical Engineering Bioengineering Computational biology Applied Microbiology and Biotechnology Genome Feces Nanopores 03 medical and health sciences 0302 clinical medicine Drug Resistance Bacterial Humans Microbiome 030304 developmental biology High resolution analysis 0303 health sciences Bacteria Microbiota High-Throughput Nucleotide Sequencing Sequence Analysis DNA Anti-Bacterial Agents Resistome Metagenomics metagenome assembler microbiome Metagenome Molecular Medicine Mobile genetic elements Software 030217 neurology & neurosurgery Biotechnology |
| Zdroj: | Nature Biotechnology. 37:937-944 |
| ISSN: | 1546-1696 1087-0156 |
| DOI: | 10.1038/s41587-019-0191-2 |
| Popis: | 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 ( |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Full text from SpringerLink