Bioinformatics solutions

We offer both standard and advanced levels of bioinformatics analysis service for Illumina Genome Analyzer projects. Please note that novel algorithms for the analysis of next generation sequencing data are becoming available at a rapid rate. As a result, there is often a range of novel software packages from which to choose. In the following sections we describe some of the most popular bioinformatics solutions for a particular analysis type. However our bioinformatics team regularly investigate novel algorithms for their suitability to data analysis, and can offer advice on the particular application that will be most appropriate for your data.

Standard Bioinformatics Service

Our Standard bioinformatics analysis service is currently included in the price of all sequencing projects. Using proprietary Illumina Pipeline software, this service includes:

• Image analysis to identify individual clusters of reads
• At each cycle of the sequencing run, using the relative intensity levels at each cluster to perform Base-Calling.
• Generation of sequence reads with associated quality scores for each base
• Generation of filtered read data, based on the per-base quality scores.
• Generation of a customised Pipeline report, summarising run statistics and quality control analysis

Advanced Bioinformatics Service

• Alignment to Reference Sequence
  • Mapping of all reads to a specified reference genome
  • Statistic report detailing coverage, orientation of mapped reads, and numbers of unmapped reads
  • Summary of coverage available in both graphical and tabular format
• Visualising sequence data within a genome browser
• Resequencing and polymorphism detection
  • Mutation detection
  • Novel mutation discovery
  • Annotation of sequence polymorphism
  • Functional analysis of target genes
• ChIP Sequencing
  • ChIP-seq analysis to determine genomic regions and peaks
  • Annotation of ChIP-seq regions and Peaks
  • Sequence motif analysis
  • Functional analyses of ChIP-seq target genes
• RNA Sequencing
  • Identification of exon splice crossing sequencing reads
  • Identification of the differences in gene expression between the control and treated samples
  • Identification of the differences in alternative splicing between the control and treated samples
  • Full gene annotation
• Small RNA Sequencing
  • Discovering microRNAs and analysis
  • Discovering novel microRNAs from deep sequencing data using RNA secondary structure information