omics2view.consulting GbR

Draw conclusions from identified mutations in your sample

Studying mutations

Accurate identification of single-nucleotide polymorphisms (SNPs), insertions/deletions (Indels) and copy number variants (CNVs) is based on unambiguous mapping data. We deliver you with variant analysis service including high quality mapping from short and long read data and confidently summarizing the detection of Indels, point mutations or CNVs of your sample, reported in variant calling format (VCF). We annotate the findings against databases and further evaluate the pathogenicity of found genetic variants.

Send your data for mapping and variance analysis, we analyse:

• Targeted (re)-sequencing data
  
• Amplicon data
  
• Whole-exome data
  
• Whole-genome data
  
• Whole-transcriptome data
  
• Affymetrix SNP Array data
  

We offer you:

• Quality check and preprocessing of FASTA/FASTQ files (454/Illumina)
  
• Mapping of data against known references with subsequent mapping report
  
• Variant calling using multiple callers
  
• Summary of results in variant caller files (VCF)
  
• Identification of homozygote/heterozygote variants
  
• Variant annotation and classification to known references
  
• Pathogenicity prediction of genetic variants

We offer statistical consulting and analyses for your scientific project. It will significantly improve the quality of your publication, theses or presentation. Among other things, we can help you with:

• Descriptive statistics
  
  • Tables
    
  • Diagrams
    
• Exploratory data analysis
  
  • Cluster analysis
    
  • Ordination in reduced space (PCA, PCoA, MDS)
    
• Tests
  
  • parametric
    
  • non-parametric
    
• Multivariate statistics
  
• Generalized linear models
  
• Linear and non-linear mixed effects models

Viruses are the most abundant biological entities on Earth. They have tremendous effects on ecosystems (as predators of prokaryotes), human health (as causative or indirect disease agents), and economy (affecting beneficial microbes in biotech processes).

Designated tools

Next-generation sequencing has raised virological studies to a new level. Viral metagenomics (viromics) reveals important information on the genetic diversity of a viral community without the need for isolating and cultivating viral species. At omics2view.consulting GbR, we apply designated analysis tools to

• identify viral genes and contigs (possibly whole genomes) in environmental metagenomes;
  
• clean viral metagenomes of contaminating host DNA;
  
• retrieve available taxonomic information;
  
• match viral metagenomes against host (meta)genomes;
  
• discover distribution patterns in relation to environmental and clinical conditions.

Fungi play a major role in many ecosystems, human health, and biotechnological processes (namely in food industry). Phylogenetic markers, namely Internal transcribed spacers (ITS), are commonly employed for characterization of fungal communities. Next-generation sequencing allows in-depth analysis of fungal community structure. We deliver comprehensive analyses of the structure of your fungal community in ecological and clinical samples, based on:

• ITS1 or ITS2 regions
  
• 18S rDNA (on request)
  

We use model-based multivariate statistics to determine the response of fungi to environmental factors. Moreover, we apply network analysis to unravel interactions of community members. This will help you to identify:

• Shifts in fungal community structure
  
• Habitat-specific indicator taxa
  
• Association patterns
  
• Environmental factors governing fungal distribution
  

Our experts will be happy to assist you with your project. For academic clients we procure sequencing of amplicon or genomic libraries on Illumina® MiSeq™ and NextSeq™ platforms.

Our experts will be happy to discuss your personal clinical microbiome project.

Following assembly, we identify relevant genomic features of your microbial genome and provide them in formats ready for downstream analysis. Furthermore, we provide you with Circos plots of these genomic features and take care of data submission to Genbank or DDJB.

We assemble high-quality draft genomes of your microbes of interest, both de-novo(without reference) or reference-guided. We make use of paired-end as well as mate-pair libraries to get concise assemblies.

The ability to sequence whole microbial genomes has revolutionized biology. Sequencing the genome of a microorganism is important to reveal its physiological potential or conduct comparative phylogenomic studies. We offer analysis of whole genome data resulting from individual microorganism or communities (Shotgun- Metagenomics, Shotgun Metatranscriptomics).

As experts for microbial profiling and functional analysis, we offer bioinformatic analysis services for microbiome data from:

• Amplicon sequencing data (e.g., bacterial 16S rDNA/rRNA)
  
• Shotgun metagenomics
  
• Shotgun metatranscriptomics
  

Adhering to the current gold standards in microbiome data analysis, yet flexible to respond to your needs, we accompany your clinical or ecological microbiome projects from study design to publication. For academic clients we procure sequencing of amplicon or shotgun libraries on Illumina® MiSeq™ and NextSeq™ platforms.