Klaus May, Chief Business Officer for Genomatix Software in Munich, Germany commented: "As the industry's only provider of a complete NGS data analysis capability, we are extremely pleased to be part of Illumina's effort. The majority of our current customer base is generating their NGS data on Illumina machines, and as such we are very familiar with them."
Peter Grant, Chief Executive Officer for Genomatix Software in Ann Arbor, Michigan, further commented: "Working with Illumina generated NGS data has helped us greatly in our ongoing effort to refine and further expand our analysis capabilities in this very demanding market. Being a part of the Illumina-Connect programme should help us to better focus those efforts as well as help us keep up with the rapidly expanding portfolio of Illumina NGS applications."
Besides the well established Genomatix micro-array analysis pipeline which works with output from the Illumina BeadChip platform Genomatix delivers a complete solution for the analysis of Next Generation Sequencing (NGS) data. This combined software/hardware platform consists of two units: the Genomatix Mining Station (GMS) and the Genomatix Genome Analyser (GGA).
The GMS is based on a proprietary genomic pattern recognition paradigm, or GenomeThesaurus, which allows for input of raw sequence reads plus optional quality files from any deep sequencing hardware, especially the Illumina Genome Analyser. It provides ultra fast mapping of sequences of any length - starting from 8bp - with no practical limits on the number of point mutations and/or insertions and deletions that can be taken into account during the mapping process.
Depending on the nature of the experiment, the GMS can provide SNP detection and genotyping, copy number analysis, and small RNA analysis. For ChIPseq data, the GMS delivers clustering and peak finding, and performs automated binding pattern identification. For RNAseq experiments, normalized expression values are calculated at the exon and transcript level. A special GenomeThesaurus is also provided for potential splice junctions, which allows for splice junction analysis and identification of new transcriptional units. For genomic re-sequencing and newly sequenced genomes, a de novo assembly will be provided.
The GGA delivers downstream software tools and databases for the deep biological analysis of genomic position data coming from the GMS or any other technology. It allows for easy integration and visualization in the terabytes of background annotation of the ElDorado genome database. GGA extensively annotates genomic co-ordinates and surrounding regions. Clustering and peak finding, analysis for phylogenetic conservation, large scale correlation analysis with annotated genomic elements, meta-analysis of data correlation between different experiments, pathway mining for groups of identified genes, transcription factor binding site (TFBS) analysis - identification, over-representation, binding partner analysis, framework identification, phylogenetic conservation, regulatory SNP effects - and much more are all processes carried out on the GGA.