Projects performed by GATC show that the use of one next generation sequencing technology alone does not deliver the best results for all projects. Rather a combination of two or three technologies provides a more complete, cost-effective analysis. In addition to sequencing, bioinformatic analysis is critically important for gaining an in-depth understanding of the biological significance of the sequence data. The combination, analysis and visualisation of these data are key challenges to the successful application of the Next Generation sequencing technologies.