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Microbial Nanopore Sequencing

Microbial Nanopore Sequencing

Overview

We use the technologies developed by the Oxford Nanopore for genome sequencing, 16S rRNA sequencing, epigenomics, and transcriptomics. Our experienced and professional team executes each procedure with high standard to analyze and provide comprehensive and accurate data.

Our Advantages:

Comprehensive analysis content, which could satisfy diverse requirements of analysis and sequencing.
Ultra-long reads (N50 > 150 Kb, read lengths up to 2 Mb).
Deliver direct DNA/RNA sequencing, as well as PCR or PCR-free cDNA sequencing.
No DNA polymerase, ligase, or dNTPs are required.
Experienced and professional team provides comprehensive and accurate bioinformatics analysis.

Tell Us About Your Project

We are dedicated to providing outstanding customer service and being reachable at all times.

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Introduction to our Nanopore sequencing

The nanopore sequencing technology detects the real-time electric current of single-stranded DNA (ssDNA) as it passes through a small protein channel, or the nanopore. The electric current data is then converted into a corresponding sequence. This technology relies on the physicochemical properties of ssDNA rather than enzymatic reactions. The sequencing speed has been greatly improved compared with next-generation sequencing systems. MinION is the only portable, real-time device for DNA and RNA sequencing on the market. The average reading length of nanopore technology can reach tens to hundreds of Kb, and the longest reading length can reach 2 Mb. Highly contiguous genome assembly can be generated for many large and complex organisms that are deemed inaccessible to NGS methods. As a result, nanopore sequencing could provide a more complete view of the genetic content and variation.

In addition to improving read length and sequencing speed, nanopore sequencing could reduce or eliminate sequencing bias caused by PCR amplification. The anopore sequencing has significantly improved de novo genome assemblies, detection of genomic structural variant, and transcriptome studies. The real-time streaming of sequence data allows for rapid insight into samples, on-demand sequencing, and dynamic workflows. We are dedicated to offering diverse microbial genomics services in the following four aspects: genome analysis, 16S rRNA sequencing, epigenomics, and transcriptomics. Problems such as complex genome assembly, and detection of structural variations can all be solved with the nanopore sequencing.

Nanopore sequencing analysis workflow

Bioinformatics Analysis

Bioinformatics Analysis		Details
Genome Analysis	Genome assembly	Determine the sequence of a genome using only randomly sampled sequence fragments
	Mutation detection	Detection of SNPs, indels, and CNVs
	Structural variation	Reveal mutational mechanisms and risk factors for chromosome rearrangement
Transcriptomics Analysis	Gene isoform identification	Detection, prediction, and characterization of RNA isoforms
	Relative abundance of transcripts	Estimation and visualization of the relative abundance of mRNA transcripts
	Identification of AS events	Identification and characterization of alternative splicing (AS) events
	SNP calling	Detection of single nucleotide polymorphisms (SNPs)
	Expression analysis	Detection of differentially expressed mRNA, lnRNA, circRNA, genes
16S rRNA Sequencing Analysis	Taxonomic assignment	OUT clustering and filtering, taxonomic assignment
	Phylogeny analysis	Construct phylogenetic trees illustrating the evolutionary relationships among species
	Statistical analysis	PCA, Heatmap, VENN analysis, etc.
Epigenomics Analysis	Data processing	Exportation of sequence data and data processing such as adapter trimming
	Alignment and assembly	Genome assembly and polishing using NGS data
	Methylation detection	N6-methyladenine (m6A), 5-methylcytosine (m5C), and N4-methylcytosine (m4C) motifs, etc.
Custom Analysis		More data mining upon your request

Sample Requirement

1. DNA: > 5 µg at a concentration of 100 ng/µl, OD_260/280 = 1.8. OD_260/230 = 2.0 - 2.2. Average fragment size > 30 kb.
2. No detergents or surfactants in the buffer. 10 mM TRIS (pH = 8.0 - 8.4) is recommended.
3. RNA: >1 µg at a minimum concentration of 50 ng/µL, RIN > 8.0, OD_260/280 ≈ 2.0, OD_260/280 = 2.0 - 2.2. No detergents or surfactants in the buffer.

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.

* For Research Use Only. Not for use in diagnostic procedures or other clinical purposes.