CAGEF provides a range of in-house data analysis and bioinformatic services for all our applications from whole genome DNA sequencing to microbiome studies. Whether you want a basic breakdown of your data or a detailed comparative analysis, our experienced team of bioinformatics specialists can support your research goals. Of course if you prefer to run your own analyses, you can check out our resource page for helpful links and information.

For all our services, customized analyses are available on request.

Microbiome, Metagenomic, and Metatranscriptomic analyses

Basic Microbiome Analyses:

  • FASTQ sequence files
  • Operational Taxonomic Unit (OTU) tables

Advanced Microbiome Analyses:

  • Alpha-diversity and beta-diversity measures
  • PCoA plots
  • Additional analyses possible in consultation with bioinformatician

Metagenome Analyses:

  • Identification of the metabolic potential of the sample
  • Generating metagenome assembled genomes

Metatranscriptome analyses:

  • Metatranscriptome assembly and annotation
  • Abundance of gene expression in known species

Genomics and Transcriptomics

Basic Analyses:

  • Demultiplexing, adaptor removal and quality trimming – FASTQ sequence files

Advanced Genomic Analyses:

  • De novo assembly
  • Read mapping to reference genome
  • Genome annotation
  • Variant (SNP / SNV) calling
  • Phylogenetic and evolutionary analyses
  • Genome-wide association studies (GWAS)
  • Network analysis
  • Multi-locus sequence typing (MLST) analysis

Additional Advanced Analyses:

  • ChIP-Seq analysis
  • Bisulfite sequencing analysis
  • Next-generation mutation mapping
  • QIS-Seq 

The CAGEF-supported Bio-Analytic Resource (the BAR) provides user-friendly web-based tools for exploring functional genomics and other data. BAR tools are designed with the plant (mainly Arabidopsis) researcher in mind, but can be useful to the wider research community.