The food industry is governed by strict laws and regulations, which provide certainty that each product meets health and safety standards. In addition to existing biochemical food product analysis, we propose a metagenomic approach. Main benefit of this approach is the ability to perform next generation sequencing as a standard first step and then align the sampled data to genomes references of many organisms suspected to be present in the sample. Additionaly, if another organism is suspected at a later date, it is easy to reause the sampled data set to perform another analysis – in the biochemical analysis this would require expensive sample storage and performing more laboratory tests. We examined three approaches to metagenomic analysis – BLAST, Centrifuge and BWA MEM.
We developed workflow utilizing Blast and Centrifuge toolkits, that is able to provide precise metagenomics information about food composition, from comparing DNA reads with reference genomes of various species. Our workflow is optimized to work on Google Cloud instance (Compute Engine) with 24 CPUs and 200 GB of RAM.