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Microbial De Novo Sequencing

Service Overview
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microbial de novo sequencingUsing de novo sequencing to obtain the genomic information of microbes provides a fresh start for exploring the genetic structure and functions, studying the evolutionary origin of microbial populations, as well as developing potential applications of these abundant microbes in medicine, disease, agriculture and environment.

Novogene is at the forefront of de novo sequencing as it becomes more rapid and affordable. Novogene’s founder, Dr. Ruiqiang Li, is a leading genomics expert and a primary developer of the SOAPdenovo software package for genome assembly. Dr. Li and the Novogene team have contributed to many important publications on novel genome sequences, and we can provide you with the high level of expertise required for your specific project.

For microbial genome, Novogene offers de novo sequencing service using both PacBio and Illumina platforms. We provide multifaceted sequencing services including genome survey, frame map, complete map and fine map tailored to different research needs. For each project, our scientists will design the best sequencing strategy utilizing an optimal combination of short reads and long-range sequence information to achieve the most comprehensive de novo assembly results for your genome of interest.

The Novogene Advantage

  • Highly experienced: We have completed over 2000 microbial sequencing projects with 20 publications on top tier journals.
  • Largest sequencing capacity: We have the largest Illumina and PacBio sequencing capacities in the world, allowing us to provide high quality data, fast turnaround, and affordable prices.
  • Project Workflow


    Sequencing Strategy & Data Quality Guarantee


    Genome CharacteristicsSequencing PlatformSequencing StrategyDelivered Data ParametersApplicationTurnaround Time (TAT)
    Bacterial frame map HiSeq PE150350 bp library ≥ 100X - Large scale samples, fast scanning25 working days
    Bacteria fine genome map HiSeq PE150350 bp library ≥ 100X
    6 Kbp library ≥ 100X
    ≤30 scaffolds Middle scale samples, somewhat fine mapping35 working days
    Bacteria complete genome map PacBio≥ 50X PacBio reads1 Scaffold, 0 gap Small number of samples, fine mapping45 working days
    Fungi survey HiSeq PE150350 bp library ≥ 100X-Estimate genome size and evaluate assembly difficulties25 working days
    Fungi frame genome map HiSeq PE150350 bp library ≥ 100X-Large amount of samples, frame mapping35 working days
    Fungi fine genome map PacBio & HiSeq PE150≥ 20X Illumina reads +
    ≥ 70X PacBio reads
    Contig N50 ≥ 1Mb
    (genome size < 100 Mb)
    Contig N50 > 500Kb
    (genome size ≥ 500 Kb)
    Small number of samples, fine mapping55 working days

    Customized services are also available upon request. Please contact us for more information.

    Sample Requirements

    • DNA amount for survey: ≥ 10 µg
    • DNA amount for genome de novo sequencing per library: ≥ 2 µg (for Illumina sequencing) and > 20 µg (for PacBio sequencing)
    • DNA concentration: ≥ 50 ng/µL (for Illumina sequencing) and > 80 ng/µL (for PacBio sequencing)
    • Purity: OD260/280 = 1.8 - 2.0 without degradation and RNA contamination
    • *DNA amount quantified by Qubit 2.0. Please consult our team for total DNA amount requirements for your strategy of interest.

The following study utilized Novogene's de novo sequencing services.

Comparative genomics identifies the Magnaporthe oryzae avirulence effector AvrPi9 that triggers Pi9-mediated blast resistance in rice
New Phytologist, 206: 1463-1475 (2015)

Rice blast, caused by the fungus Magnaporthe oryzae, is a significant threat to stable rice production worldwide, and yet the virulence mechanisms of this fungus remain poorly defined. In this study, a virulent strain and an avirulent strain of Magnaporthe oryzae were sequenced using Novogene’s HiSeq platform, and the genomes were assembled de novo with our SOAPdenovo program. Comparative genomics revealed an insertion within the coding sequence of the avirulent effector AvrPi9 in the virulent strain, a disruption that turns off the rice Pi9-mediated blast-resistance mechanism. This study highlights the effectiveness of applying comparative genomics with de novo microbial sequencing data for elucidating key mechanisms in the pathogenesis of fungi.


Figure. Genomic structure of the AvrPi9 locus in Magnaporthe oryzae
  Whole Genome Sequencing on HiSeq X (Human/ Animal/ Plant)
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