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Informatics analysis

Analysis of NGS datasets tend to be both complex and computationally intensive, and can be very daunting for those unfamiliar with handling these data.

The CGR informatics team have many years of expertise in this field and can assist collaborators with their projects, from offering guidance on experimental design through to performing complete analyses.

Tailored bioinformatics support which covers genome and transcriptome assembly, annotation, variant detection, epigenetics (base modification), differential gene expression analysis, microbial community taxonomic profiling (16S and 18S rRNA) and functional metagenomics and metatranscriptomics.

Throughout the project, we will update you with progress and provide a full project report, detailing techniques used and results.

Analyses

We provide expertise in a broad range of informatic analyses on data from a multitude of sequencing platforms, including:

  • De novo genome and transcriptome assembly, with subsequent gene prediction and annotation.
  • Detection of variants from genomic data, including SNPs, insertions/deletions, somatic variants, copy number variants and large structural variants.
  • Differential gene/transcript expression analyses with subsequent mapping of results to functional pathways (KEGG and GO)
  • Metagenomics/metatranscriptomics analysis (whole genome/transcriptome), to determine taxonomic and/or functional composition of prokaryotic and viral populations
  • Metagenetics (e.g. 16S amplicon analysis) to taxonomically profile samples and detect differences in diversity resulting from changes in experimental conditions
  • Epigenetics, to detect methylated/modified bases and motifs, and identify differential methylation between samples.
  • ChIP-seq analysis, including the detection of differences between samples groups
  • Our analysts can provide bespoke analyses and are happy to discuss your project requirements.

Quality assessment of data

All data sequenced with the CGR undergo quality assessment to ensure that everything looks ok with your data. We will process sequences to remove any low quality reads and remove adapter sequences so it is ready for downstream processing whether by the collaborator or by us. Once they are ready, all sequence data and results are available for download from a secure web link, and stored on our servers for at least 6 months.

Project design

If you are unfamiliar with handling NGS data, it can be difficult to know what informatic support may be required. We encourage our clients to discuss their potential requirements with us at the outset but we can also provide additional analyses after a project has been completed. Please contact us if you would like to discuss data analysis options.

Training

The team run workshops through the year to train researchers in various informatic techniques: Ideal for if you would like to prepare to analyse your own data, or simply to gain a better understanding of the field. Also, we are always happy to discuss and explain the analyses we carry out for you, both before, during and after the project.