Rapid Microbial Strain Identification in the Cloud

Perform fast, accurate microbial strain identification using whole genome maps with Microbial Explorer.

Microbial Explorer™ (ME) is an advanced, cloud-based microbial strain identification software for the Nabsys HD-Mapping platform. ME combines our microbial genomic structural analysis pipeline with the power of the cloud to dramatically reduce analysis time, lower informatics costs and improve microbial strain identification in a simple to use interface accessed through a web browser. ME is particularly effective for those that have limited access to informatics infrastructure and are looking to decrease IT costs while improving microbial strain identification.


16S rRNA gene amplicon and shotgun metagenomic sequencing have emerged as the main approaches for microbiome analysis. 16S for cost effective sample throughput, and shotgun for its cost effective high complexity across bacteria, virus, and fungi. The limitations of these methods are well documented whether it be 16S lacking in specificity, or shotgun’s limited sample throughput. Additionally, the need for computationally intensive contig assembly slows throughput and adds cost. Most importantly, both approaches utilize short reads limiting their ability to identify large structural differences that can be critical to increased specificity, particularly in low abundance or complex samples.

HD-Mapping is a single molecule technology that generates reads up to 300 kbp compared to 700 bp that is typical in shotgun sequencing. These long reads are analyzed to identify highly unique genomic structural differences in microbial samples which are compared to the reference database without the need for assembly. This approach dramatically improves both specificity, allowing resolution of highly related strains even when present in low abundance, and throughput. This means that more samples can be run with higher accuracy in a shorter time and at a lower cost. ME in conjunction with HD-Mapping provides a highly specific and rapid solution for strain identification of complex microbial samples with clear and concise visuals.


Secure – built in the Google cloud ME benefits from the very latest and best encryption and cloud security. Click here to learn more about ME security.

Fast – The latest version of the NCBI bacterial genome database is pre-loaded and because ME lives in the cloud there is virtually no limit to the dynamic compute resources that can be allocated to a project. This brings analysis times down to a few minutes and you can process many samples simultaneously.

Simple – an intuitive web-based user interface allows researchers to upload, run, and analyze results without bioinformatics expertise or support.

Affordable – There is no need for expensive hardware or network configuration and the speed that’s gained from high-performance cloud computing (HPC) keeps costs down allowing Hitachi to offer HCE at a low, predictable fixed rate.


Nabsys HD-Mapping whole meta genome datasets are imported into ME. High label density long reads are aligned against a pre-loaded version of the latest NCBI bacterial genome database to match unique structural differences between the sample and reference. By pre-loading and indexing the reference database ME eliminates the most time-consuming part of microbial strain identification analysis. The process performs further analysis considering both the degree of uniqueness and the amount of coverage of the reference. ME also exploits the use of high-performance cloud computing (HPC) and is optimized for the lowest possible network latency. The result is the ability to resolve sub-strain identification of all microbes present in the sample within minutes.