Services & Support

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Bacterial Whole Genome Analysis

Whole Genome Sequencing

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Bacteria, Archaea, Fungi and Viral Genome Analysis

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More Accurate Results with Long Reading

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Variations between Strains by Comparative Analysis

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Project Based Analysis and Methodology

Whole genome analysis is a method of genetic analysis that provides a comprehensive examination of an organism’s entire genome and functional genes. With this analysis, changes in positions where the genome of the organism differs from the reference genome, namely variants, are detected. Antimicrobial resistance genes, secondary metabolite genes and virulence genes are detected in the annotated genome.

  • Alignment image
  • Image of circular genome with functional genes
  • Genome comparison analysis with close subspecies (BRIG)
  • Polymorphism table
  • Antimicrobial resistance genes
  • Secondary metabolite genes
  • Virulence genes
  • LASTZ-Mauve multi-sample genome alignment analysis

Antimicrobial Resistance Analysis(AMR)

Antimicrobial resistance (AMR) is an important global health problem. Metagenomics enables the analysis of resistomes in various microbial ecosystems.

With shotgun metagenomic sequencing and whole genome sequencing, antibiotic resistance genes are detected with long reads using Oxford Nanopore Technologies. Resistome detection is performed within raw data using the Comprehensive Antibiotic Resistance Database (CARD).

Metagenomic Analyzes

Massive Bioinformatics specializes in metagenomic analyses that make use of Oxford Nanopore technology. We provide the following services based on your project requirements:

 

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Comparative Analysis and Data Visualization:

 We provide comparative analysis of samples for population research and biomarker discovery. We also give visually appealing graphical presentations that are relevant to the subject of your research.

Metagenomic analyzes of bacteria and archae groups with 16s rRNA gene, fungi with ITS region, and eukaryotic organisms with 18S rRNA gene are performed by using barcode genes for different living groups. It is possible to use different databases according to the content of the study, combinations with different workflows to increase the accuracy of the results are among the services we provide.

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Comprehensive Metagenomic Analysis:

 We perform metagenomic analyses on bacteria and archaea (using the 16S rRNA gene), fungus (using the ITS region), and eukaryotic species (using the 18S rRNA gene). This is accomplished by employing barcode genes unique to each group. 

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Custom Database and Workflow:

To ensure the maximum possible accuracy of the results, we can adapt the databases and workflows employed based on the specific requirements of your study. Metagenomic analyzes of bacteria and archae groups with 16s rRNA gene, fungi with ITS region, and eukaryotic organisms with 18S rRNA gene are performed by using barcode genes for different living groups. 

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Species Identification:

 Using Oxford Nanopore technology, we deliver high-resolution species identification by sequencing the full 16S rRNA gene (1500 bp) not only the hypervariable V3-V4 region (450 bp), allowing for greater taxonomic precision. This strategy dramatically reduces the error rate associated with short-read sequencing technologies that only target ~450 bp of the gene.

Shotgun Metagenomics

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All Genes Found in the Environment

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More Accurate Results with Long Reading

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Viral Metagenomics

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Whole Genome Construction from Metagenomik Data

Shotgun Metagenomic analysis makes possible to access all nucleic acid information contained in a sample. All of the total genomic material obtained by this method is sequenced and then the desired information is reached with the databases for target organism groups or genes. The amount of data to be obtained and the methods of analysis vary according to the content of the sample and the desired information. Massive bioinformatics provides shotgun metagenome analysis with both short readings and long readings.

SSu – LSu Metagenomics Analyses

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More Accurate Metagenome Results with Long Reading

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Bacteria, Archaea, Eukaryotes and Fungi

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Metagenomics with 16S rRNA, ITS, 18S rRNA Genes

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Comperative Metagenomics Analyzes

Metagenomics analyzes make possible to determine the diversity and amounts of microorganisms in a sample. Identification of bacteria with the 16S rRNA gene with a length of ~ 1500 bp is now a standardized process. However, most of the new generation sequencing methods used only a portion of this gene which is approximately ~ 450 bp in length and therefore produce erroneous results. Oxford Nanopore enhanced the resolution of species identification by reading the entire 1500 bp 16S rRNA gene thanks to its long reading technology and opened a new page in this field. Metagenomic analyzes provide a large number of possibilities for detailed examination of a wide variety of sample types, or components of a sample.

Amplicon Sequencing

Massive Bioinformatics specializes in metagenomic analyses that make use of Oxford Nanopore technology. We provide the following services based on your project requirements.

 

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Whole Amplicon Sequence With Long Read Technology

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Primer Design For Desired Regions

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Multiple Region Analysis in a Single Run

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Project Based Analysis and Methodology

Discover with our Amplicon Sequencing Service – a targeted genetic analysis solution designed to unlock precise insights from DNA or RNA samples. By selectively amplifying and sequencing specific regions of interest, we provide you with focused, high-resolution data, perfect for pinpointing mutations, unraveling genetic diversity, and tracking variations. Our cutting-edge technology ensures accurate results even from limited genetic material, empowering you to make informed decisions swiftly and cost-effectively. From medical breakthroughs to environmental exploration, our Amplicon Sequencing Service is your pathway to streamlined, impactful genetic analysis.

RNA Sequencing

 

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Direct RNA Sequencing

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Analysis of Total RNA Profiles

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Project Based Analysis and Methodology

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Hypothesis Tests With Comparative Analyses

Our Services Laboratory offers RNA-Seq services for a wide range of analyses, including differential gene expression (DEGs), fusion gene discovery, and variant identification, including single nucleotide variations (SNVs) and insertions/deletions (Indels). These assessments are carried out by our skilled bioinformaticians using cutting-edge technology and best-in-class algorithms. Our bioinformatics solution enables a high-level overview and detailed data exploration by showing important expression patterns in your RNA data, complemented by heatmap and PCA (Principal Component Analysis) analysis. Enrichment analysis using databases like KEGG, GO, DO, Reactome, and WikiPathways also provide useful insights into the functional implications of your RNA data.

Viral Whole Genome Analysis

Viral whole genome sequencing using the Oxford Nanopore methodology is a cutting-edge and innovative technique that enables comprehensive analysis of viral genetic material. Leveraging the power of nanopore sequencing technology developed by Oxford Nanopore Technologies, this approach provides researchers and scientists with a high-resolution view of the complete viral genome

 

COVID-19 Analysis

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Phylogeny and Transmission Analysis

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More Accurate Results with Long Reads

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Viral Metagenomics

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Whole Genome Construction from Metagenomic Data

With our customized pipeline for detection of SARS-CoV-2 based on Oxford Nanopore sequencing technology which utilizes the benefits of long reads. Our service aligns the reads to SARS-CoV-2 reference genome, calls variants, and generates a consensus genome sequence. It then determines lineage, clade and phylogenetic tree information of the sample using Pangolin and NextClade. All the information with its data and QC metric files gets summarized in one extensive html report for easy viewing.

Influenza Analysis

Oxford Nanopore Technologies offers a workflow that enables Influenza A and B whole genomes to be amplified by PCR and run 96 different samples in a single flow cell using ligation sequencing chemistry.

Sequencing data of influenza samples are used with our automated analysis program to determine which subtype the Influenza genome belongs to via the Nextclade database (clades.nextstrain.org). The studied data are evaluated and reported with the vaccine strains of Influenza A and B virus types in this database.