ArticleScientific reports2016
Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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76 citing papers in PubMed.
- Opportunities for RNA sequencing in physiology: from big data to understanding homeostasis and heterogeneity.Function (Oxford, England) · 2026Review
- Metagenomic Assembly and Gene Prediction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Reference-guided assembly of metagenomes with MetaCompass.Cell reports methods · 2025Article
- Metagenomics Disentangles Differential Resistome Traits and Risks in Full-Scale Anaerobic Digestion Plants under Ambient, Mesophilic, and Thermophilic Conditions.ACS environmental Au · 2025Article
- HyLight: Strain aware assembly of low coverage metagenomes.Nature communications · 2024Article
- Step-by-Step Metagenomics for Food Microbiome Analysis: A Detailed Review.Foods (Basel, Switzerland) · 2024Review
- Sample and Library Preparation for PacBio Long-Read Sequencing in Grapevine.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Comparing genomes recovered from time-series metagenomes using long- and short-read sequencing technologies.Microbiome · 2023Article
- Article
- Long-Read Metagenomics and CAZyme Discovery.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes.mSystems · 2022Article
- Novel Virus Identification through Metagenomics: A Systematic Review.Life (Basel, Switzerland) · 2022Review
- Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing.Nature methods · 2022Article
- Characterization of the cecal microbiome composition of Nigerian indigenous chickens.Tropical animal health and production · 2022Article
- Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter.Environmental microbiology · 2022Article
- High-Resolution Metagenomics of Human Gut Microbiota Generated by Nanopore and Illumina Hybrid Metagenome Assembly.Frontiers in microbiology · 2022Article
- A Journey on the Skin Microbiome: Pitfalls and Opportunities.International journal of molecular sciences · 2021Review
- Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing.NPJ biofilms and microbiomes · 2021Article
- Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes.Scientific reports · 2021Article
- The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology.Scientific reports · 2021Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
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Abstract
DNA assembly is a core methodological step in metagenomic pipelines used to study the structure and function within microbial communities. Here we investigate the utility of Pacific Biosciences long and high accuracy circular consensus sequencing (CCS) reads for metagenomic projects. We compared the application and performance of both PacBio CCS and Illumina HiSeq data with assembly and taxonomic binning algorithms using metagenomic samples representing a complex microbial community. Eight SMRT cells produced approximately 94 Mb of CCS reads from a biogas reactor microbiome sample that averaged 1319 nt in length and 99.7% accuracy. CCS data assembly generated a comparative number of large contigs greater than 1 kb, to those assembled from a ~190x larger HiSeq dataset (~18 Gb) produced from the same sample (i.e approximately 62% of total contigs). Hybrid assemblies using PacBio CCS and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length and number of large contigs. The incorporation of CCS data produced significant enhancements in taxonomic binning and genome reconstruction of two dominant phylotypes, which assembled and binned poorly using HiSeq data alone. Collectively these results illustrate the value of PacBio CCS reads in certain metagenomics applications.
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