We utilize the advanced PacBio SMRT instruments in microbiology for several research purposes including microbial genome analysis, full-length 16S rRNA sequencing, metagenomics, transcriptomics, and epigenomics. Our experienced and professional team executes quality management following each procedure and provides comprehensive and accurate data and bioinformatics analyses.
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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 nucleotides that are incorporated, 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 sequence and analyze the genomes of microbial species, ranging from viruses to prokaryotes. More and more researches have confirmed the advantages of PacBio SMRT sequencing in complex microbiology, including long reads, high consensus accuracy, a low degree of bias, and simultaneous detection of epigenetic modifications. 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. Based on our PacBio SMRT sequencing platform, we are dedicated to providing microbial genomics services in the following four aspects: 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/clinical 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.
Our bioinformatics analyses are flexible to your specific projects.
|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|
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.