Expertise offered by the Sheffield Bioinformatics Core

The SBC has expertise in the following areas, and software packages:-

Experimental Design

If you are planning an experiment, please come to us before generating data so that we can discuss the design

The Core is experienced in advising on the following issues:-

  • Optimal number of replicates
  • Biases and confounding factors
  • Single-end or paired-end sequencing
  • Depth of sequencing required

High-Throughput Sequence Analysis

  • BWA, Bowtie and other aligners for all NGS platforms and applications
  • Tophat, edgeR, DESeq2 and salmon (among others) for RNA-Seq analysis
  • GATK, VarScan and MuTect for somatic and germline mutation calling
  • manta, BRASS for calling of structural variants
  • MACS2, and other peak callers for ChIP-Seq analysis
  • Downstream analysis of gene lists to identify over-represented pathways / ontologies using GSEA, goseq, or other online tools such as DAVID or Genetrail.

Nanopore Sequence Analysis

  • Direct & cDNA RNASeq
  • CRISPR/Cas9 targeted sequencing
  • Amplicon sequencing
  • SARS-CoV-2 sequencing and analysis
  • Microbial genomics
  • Plasmid sequencing

Clinical Bioinformatics Services

Matthew Parker is a registered Clinical Scientist (Bioinformatics) in the core and has experience of providing clinical bioinformatics services for the NHS.

  • Clinical bioinformatics consulting:
    • Consultation on appropriate and best practice clinical bioinformatics
    • Staff training in bioinformatics
    • Advice/Implementation of computing facilities for clinical analysis
    • Consultation on obtaining UKAS (ISO-15189) accreditation
  • Extended variant review and analysis
  • Analysis of copy number and structural variants
  • Assessment of analyses and pipelines
  • Integration of bioinformatics pipelines with other software, e.g. LIMS
  • Ad-Hoc bioinformatics support

Microarray Analysis

  • Experience with data from Affymetrix and Illumina platforms
  • Varying data types, including expression, methylation (450K), SNP and copy-number

Further Expertise

  • Custom pipeline creation
  • Custom visualisation of high-throughput data
  • Packaging and deploying software environments with docker
  • Data Management and curation
  • Creating interactive web applications wih shiny

As well as these analysis services, we also provide training courses and bespoke 1-to-1 training for researchers