About MicrobeGPS

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What is MicrobeGPS?

MicrobeGPS is a bioinformatics tool for the analysis of metagenomic sequencing data. The goal is to profile the composition of metagenomic communities as accurately as possible and present the results to the user in a convenient manner. One main focus is reliability: the tool calculates quality metrics for the estimated candidates and allows the user to identify false candidates easily.

MicrobeGPS is a reference based taxonomic profiling tool. This means that it works with reference genomes of known microbial organisms. However, the strength of MicrobeGPS is that it does not need the exact genome to be present in the database. If the database only contains a similar or distantly related genome, MicrobeGPS is still able to find it and indicates visually that the database genome doe not match perfectly. This is what we call the [GPS principle].

Applications

Taxonomic profiling

MicrobeGPS was designed as a taxonomic profiling tool that is accessible also to non-specialists. Some applications ranging from profiling of microbial communities with varying complexity to clinical applications for identifying an infectious agent are reported in our publication in PLOS ONE:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117711

Finding contaminations

We also used MicrobeGPS for finding contaminations in NGS datasets. The genome validity and the homogeneity score turned out to be useful to decide whether read mappings to a reference genome are due to sequence homology or contamination in the sample.

For example, in an amoeba genome assembly project, we used MicrobeGPS to check the Illumina sequencing dataset for rat contamination, since the amoeba was grown on rat cells. With MicrobeGPS, we could assure that the reads mapping to the rat genome, although being high quality matches, are very unlikely to originate from the rat DNA. Since the reference genome is not yet available (it's an assembly project), there was no other easy way to find this out.