{"doi":"10.1038/s41587-019-0191-2","title":"Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes","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 (<1%) with ~9× long-read coverage and near-complete genomes with higher coverage. We used OPERA-MS to assemble 28 gut metagenomes of antibiotic-treated patients, and showed that the inclusion of long nanopore reads produces more contiguous assemblies (200× improvement over short-read assemblies), including more than 80 closed plasmid or phage sequences and a new 263 kbp jumbo phage. High-quality hybrid assemblies enable an exquisitely detailed view of the gut resistome in human patients.","journal":"Nature Biotechnology","year":2019,"id":7429,"datarank":0.9088684793372697,"base_score":6.059123195581797,"endowment":6.059123195581797,"self_citation_contribution":0.9088684793372697,"citation_network_contribution":0.0,"self_endowment_contribution":0.9088684793372697,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":427,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0463,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2019-07-29","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":23990,"name":"Jim Shaw","orcid":"0000-0002-6990-7829","position":1,"is_corresponding":false},{"id":66065,"name":"Manesh Kalathiyappan","orcid":null,"position":2,"is_corresponding":false},{"id":66066,"name":"Amanda Hui Qi Ng","orcid":"0009-0008-1604-9876","position":3,"is_corresponding":false},{"id":66067,"name":"M. Senthil Kumar","orcid":null,"position":4,"is_corresponding":false},{"id":66068,"name":"Chenhao Li","orcid":"0000-0003-1182-6804","position":5,"is_corresponding":false},{"id":66069,"name":"Mirta Dvornicic","orcid":null,"position":6,"is_corresponding":false},{"id":66070,"name":"Janja Paliska Soldo","orcid":null,"position":7,"is_corresponding":false},{"id":66071,"name":"Jia Yu Koh","orcid":"0000-0001-8772-8392","position":8,"is_corresponding":false},{"id":66072,"name":"Chengxuan Tong","orcid":null,"position":9,"is_corresponding":false},{"id":66073,"name":"Oon Tek Ng","orcid":"0000-0002-9569-2315","position":10,"is_corresponding":false},{"id":66074,"name":"Timothy Barkham","orcid":"0000-0003-0975-2244","position":11,"is_corresponding":false},{"id":66075,"name":"Barnaby Young","orcid":null,"position":12,"is_corresponding":false},{"id":66076,"name":"Kalisvar Marimuthu","orcid":"0000-0002-0395-5633","position":13,"is_corresponding":false},{"id":66077,"name":"Kern Rei Chng","orcid":"0000-0003-2746-9880","position":14,"is_corresponding":false},{"id":66078,"name":"Mile Sikic","orcid":"0000-0002-8370-0891","position":15,"is_corresponding":false},{"id":12436,"name":"Mushthofa Mushthofa","orcid":"0000-0003-4991-4148","position":16,"is_corresponding":false},{"id":66079,"name":"M. S. Binoj Kumar","orcid":null,"position":17,"is_corresponding":false},{"id":66080,"name":"Mirta Dvorničić","orcid":null,"position":18,"is_corresponding":false},{"id":66081,"name":"Barnaby Edward Young","orcid":"0000-0003-1010-2230","position":19,"is_corresponding":false},{"id":12266,"name":"Andreas Bender","orcid":"0000-0002-6328-7104","position":0,"is_corresponding":true}],"reference_count":73,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}