Bioinformatics

CAGEF provides a range of in-house data analysis and bioinformatic services for many of 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

Depending on the analyses required for your study, we offer three analysis options:

Basic FASTQ file generation

  • No additional analyses, FASTQ sequences generated by the Illumina pipeline.

Microbiome analyses

  • Operational Taxonomic Units (OTUs) with taxonomies assigned
  • Taxonomic analysis and relative abundance
  • Alpha-diversity and Beta-diversity

Metagenome analyses

  • Metagenome assembly and annotation
  • Distribution of genes in known species

Metatranscriptome analyses

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

Whole Genome, Transcriptome, and related Next-Gen Sequencing

Demultiplexing, adaptor removal, and quality trimming

  • No additional analyses, FASTQ sequences generated by the Illumina pipeline

Genome assembly

  • De novo assembly
  • Read mapping
  • Genome annotation
  • Next-Gen mutation mapping

Advanced Next-Gen analyses

  • Variant (SNV/SNP) calling
  • Phylogenetic and evolutionary analyses
  • Genome-wide association studies (GWAS)
  • Network analysis
  • RNA-Seq analysis, including differentially expressed genes, GO enrichment, and alternative splicing
  • ChIP-Seq analysis
  • Bisulfite sequencing analysis
  • Multi-locus Sequence Typing (MLST) analysis

 


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