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Nanopore-Based Microbial Genome Sequencing


We offer microbial genome analysis based on nanopore sequencing from the Oxford Nanopore Technologies (ONT) to identify DNA bases by measuring the changes in electrical conductivity as DNA strands pass through a biological pore. We are dedicated to ensuring long and unbiased sequence reads for microbial whole-genome assembly and analysis, without amplification or chemical reactions.

Our Advantages:
  • High-throughput, low cost, and long-read sequencing.
  • Real-time sequencing directly targeting single DNA molecules.
  • Time-saving, simplified workflow.
  • Flexible bioinformatics pipelines.
  • Fast turnaround times and a highly experienced expert team.
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Nanopore-based genome analysis platform

In recent years, there have been enormous achievements made in DNA sequencing technologies, including the next-generation sequencing (NGS), 3rd-generation sequencing (also known as long-read sequencing), and corresponding innovations in bioinformatics analysis. Those achievements are driving the development of an exciting field of biological research called genome analysis. Oxford nanopore sequencing identifies DNA bases by measuring the current changes in electrical conductivity as nucleic acid molecules pass through a biological pore in membranes, generating much longer average reads (ultra-long reads, over 800,000 bases) than other DNA sequencing technologies. Our nanopore-based microbial genomics analysis can generate ultra-long reads (about 5.4 kb to 10 kb of average read length) that span challenging genomic regions. We also polish the microbial genome assembly with short reads generated by the Illumina system to improve accuracy even to 99.96%.

Our nanopore-based microbial genome analysis services include microbial whole-genome sequencing and targeted sequencing, along with comprehensive bioinformatics tools to reconstruct bacterial, fungal, or viral genomes (de novo) and perform further genome-based analysis. With highly precision and complete genome assemblies, it is possible to perform accurate microbial identification, elucidate genome structures, identify variants (phage insertion, transposon insertion, SVs, InDels, SNVs) in the evolution of virulence, understand the role of mobile elements in drug transmission and resistance, and annotate gene function. We are dedicated to helping you generate high-quality, closed reference genomes, redefining the extent of genetic diversity, and elucidating microbial genetics and evolution.

Nanopore-based microbial genome analysis workflow

Bioinformatics Analysis

Our bioinformatics analysis includes raw data quality control, genome assembly and polishing, genome annotation and analysis, comparative analysis, and custom analysis.

Pipelines Details
Raw data quality control Correction, classification, reduced redundancy, etc.
Genome assembly and polishing Reveals genomics sequence, gene structure and location.
Genome annotation and analysis Prediction of pathogenicity genes, susceptibility genes, and non-coding RNAs, detection of clustered regularly interspaced short palindromic repeats (CRISPRs), etc.
Comparative genomics Phylogenetic analyses, divergence-time estimation, etc.
Custom analyses More data mining upon your request

Sample Requirement

Sampling kits: We provide a range of microbial sampling kits for clients, including MicroCollect™ oral sample microbial collection products and MicroCollect™ stool sample collection products.

Deliverables: Raw sequencing data (FASTQ), trimmed and stitched sequences, quality-control dashboard, statistic data, and your designated bioinformatics report.

References

  1. Xinpeng Tian, et al. Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level. Frontiers in Microbiology. 2016, 7: 998-1104.
  2. Hans J. Jansen, et al. Rapid de novo assembly of the European eel genome from nanopore sequencing reads. SCIENTIFIC REPORTS. 2017, 7: 7213.
  3. Miten Jain, et al. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biology. 2016, 17:239.

Areas of Interest

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