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Metagenomic Sequencing-Nanopore


Metagenome refers to a collection of the total genetic material of a mixed community of organisms, such as environmental and human metagenomes. It contains genomes of both cultivatable and uncultivatable microorganisms. Metagenomic sequencing enables the study of these intricate genomic landscapes embedded in environmental samples by providing more than taxonomic profiling, also offering a functional genomics perspective by exploring the encoded genes and their putative roles in ecological processes. While traditional shotgun approaches with Illumina sequencing, have been widely used in metagenomic studies, the advent of Nanopore long-read sequencing has changed the field. Nanopore technology enhances downstream bioinformatic analyses, notably metagenome assembly, ensuring more continuous assemblies. Remarkably, reports indicate that Nanopore-based metagenomics has successfully generated complete and closed bacterial genomes from complex microbiomes (Moss, E. L., et. al, Nature Biotech, 2020). Integrating Nanopore reads with Illumina reads provides a strategic approach for error correction, mitigating Nanopore’s inherent low accuracy. This synergistic combination leverages the strengths of each sequencing platform, offering a robust solution to overcome potential limitations and advancing the precision and reliability of metagenomic analyses.

Service Details


Demo Results

Featured publications

Service Features

●  Long read sequencing on Nanopore P48 (8-10Kb library)

●  Error-correction: sequencing on Illumina NovaSeq (PE150 library)

Service Advantages

●  High-quality metagenome assembly: with less contigs that have higher continuity.

●  Higher accuracy: of species identification and functional gene prediction.

●  Improved assembly: facilitates bacterial genome isolation and comparative metagenome analysis.

         Comprehensive bioinformatics analysis: focused not only on taxonomic diversity but also on the functional diversity of the community.

●  Extensive experience: with a track record of successfully closing multiple metagenomics projects in various research domains and processing over 10,000 samples, our team brings a wealth of experience to every project.

Service Specifications

Sequencing platform

Sequencing Strategy

Data recommended

Illumina NovaSeq



Nanopore P48



Sample Requirements


Concentration (ng/µL)

Total amount (µg)

Volume (µL)



Illumina PE150 Library






Nanopore 8-10Kb library






Service Work Flow

sample delivery

Sample delivery

Library Preparation

Library construction



Data analysis

Data analysis

After sale Services

After-sale services

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  • 流程图 贝贝第三版-02

    Includes the following analysis:

    ●  Sequencing data quality control

    ●  Metagenome assembly and gene prediction

    ●  Gene annotation

    ●  Taxonomic alpha diversity analysis

    ●  Functional analysis of the community: biological function, metabolic, antibiotic resistance

    ●  Analysis on both functional and taxonomic diversity:

              Beta diversity analysis

              Inter-group analysis

              Correlation analysis: between environmental factors and OUT composition and diversity

    Non-redundant gene set distribution:

    图片68 Gene annotation: KEGG pathway


    Gene annotation: eggNOG



    Gene annotation: CAZY carbohydrates



    Species correlation network:


    Explore the advancements facilitated by BMKGene’s metagenomics sequencing service with Nanopore + Illumina with this featured publication:

    Jin, H. et al. (2023) ‘A high-quality genome compendium of the human gut microbiome of Inner Mongolians’, Nature Microbiology 2023 8:1, 8(1), pp. 150–161. doi: 10.1038/s41564-022-01270-1.

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