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Microbial PacBio SMRT Sequencing

Microbial PacBio SMRT Sequencing

Overview

We utilize advanced PacBio SMRT instruments in microbiology microbial genome analysis, full-length 16S rRNA sequencing, metagenomics, transcriptomics, and epigenomics. Our experienced and professional team provides comprehensive and accurate data and bioinformatics analyses.

Our Advantages:

Comprehensive analysis package satisfying diverse requirements of microbial genomics.
The average read lengths are over 15 kb, which could greatly accelerate the genome assembly.
High consensus accuracy, a low degree of bias, and simultaneous detection of epigenetic modifications.
Effective cost and rapid turnaround time.

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 PacBio SMRT sequencing platform

PacBio SMRT sequencing technology is novel and unique, enabling the direct, real-time observation of DNA synthesis by DNA polymerase. The zero-mode waveguides can only capture signal from incorporated nucleotides, which are fixed to the bottom of the well and allow the DNA strand to pass through them. Compared to other sequencing technologies, PcBio SMRT sequencing is an ideal tool to determine the genomes of microbial species, ranging from viruses to prokaryotes. The advantages of PacBio SMRT sequencing technology in complex microbiology, such as long reads, high consensus accuracy, a low degree of bias, and simultaneous detection of epigenetic modifications, have been recognized by many researchers. The average read length from the PacBio instrument is approximately 2 kb, and some reads may be over 20 kb. Longer reads are especially useful for de novo assemblies of novel genomes due to their ability to span repetitive regions.

PacBio SMRT sequencing technology produces HiFi reads by using the circular consensus sequencing (CCS) model for the detection of diverse variant types from single-nucleotide to structural variants, species-level classification, functional annotation, and pathway enrichment study. We provide microbial genomics services using our PacBio SMRT sequencing platform, Our services cover: genome sequencing, 16S rRNA sequencing, metagenomics, transcriptomics, and epigenomics. PacBio SMRT sequencing technology is not only an effective tool in the basic biological sciences but also in the medical settings. It has been applied to many microbial sequencing projects, including full-length viral sequencing, bacterial whole genome sequencing, long-read metagenomic sequencing, long-read amplicon sequencing of disease-associated genes/regions and so on.

PacBio SMRT sequencing analysis workflow

Bioinformatics Analysis

Our bioinformatics analyses are flexible to your specific projects.

Bioinformatics Analysis		Details
Genome Analysis	Genome assembly	High-quality de novo assemblies of genomes using Hierarchical Genome Assembly Process (HGAP)
	Functional annotation	COG, KEGG, GO, etc.
	Genome annotation	Prediction of Non-coding RNAs, detection of CRISPRs, etc.
	Evolutionary analysis	Construction of phylogenetic trees
	Variant calling	Detection and annotation of copy number variations (CNVs), structural variations (SVs), single nucleotide polymorphisms (SNPs), and insertion-deletions (InDels)
Transcriptomics Analysis	Isoform analysis	Reference genome mapping, full-length isoform correction and classification, reduced redundancy
	Functional annotation	GO,KEGG, KOG, COG, Swissport, etc.
	Gene expression analysis	Analysis of gene abundance, identification of differentially expressed genes (DEGs)
	Structure identification	Prediction of alternative splicing events, LncRNAs, miRNAs, and CDS, the discovery of novel transcripts, identification of fusion genes, etc.
	SNPs/SSRs analysis	Detection and annotation of SNPs and simple sequence repeats (SSRs)
16S rRNA Sequencing Analysis	OUT clustering	Clustering and filtering of operational taxonomic units (OTUs)
	Taxonomic assignment	Venn diagram, rank abundance curve, PCA, etc.
	Diversity analysis	Alpha diversity, beta diversity, meta analysis
	Functional prediction	PICRUSt, FAPROTAX, Tax4fun, FunGuild
Metagenomics	Assembly	Reference-based assembly, de novo assembly, and quality assessment of metagenomics assemblies.
	Taxonomic assignment	Taxonomic assignment, species abundance analysis
	Epigenomics functional annotation	Metagenome gene prediction, protein function prediction, and pathway annotation
Custom Analysis		More data mining upon your request

Sample Requirement

1. DNA: ≥ 10 ug at a concentration of 100 ng/µL
2. OD_260/280 = 1.8 - 2.0 and OD_260/230 = 2.0 - 2.2, without degradation or DNA contamination
3. RNA: ≥ 5 ug at a minimum concentration of 50 ng/µL
4. OD_260/280 = 1.8 - 2.2, OD_260/230 ≥ 1.5, 28S:18S ≥ 1.5，RIN ≥ 7, without degradation or DNA contamination

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 data files in BAM format, demultiplex CCS reads in FASTQ format, quality-control dashboard, statistic data, and your designated bioinformatics analysis report.

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