Rapid Structural Variation Analysis in the Cloud

Perform fast, accurate detection of structural variation using whole genome maps with Human Chromosome Explorer

Human Chromosome Explorer™ (HCE) is an advanced, cloud-based, whole genome map assembly and structural variation (SV) analysis software for Bionano Genomics and Nabsys HD-mapping platforms. HCE combines our true de novo assembler and SV analysis pipeline with the power of the cloud to dramatically reduce analysis time, lower informatics costs and improve SV analysis results in a simple to use interface accessed through a web browser. HCE is particularly effective for those that have limited access to informatics infrastructure and are looking to decrease IT costs all while improving SV analysis results.


Either optical or electronic genome mapping datasets are imported into HCE through a web browser with a few simple clicks. HCE then uses a true de novo assembly process to build consensus maps. This process starts by identifying high quality, long reads to use as the seeds from which contigs can grow. These seeds are fed and extended through iterative comparisons to the smaller molecules throughout the dataset - without comparison to a reference database - to achieve a truly de novo assembly. This process also uses more of the available reads, which may allow for higher accuracy at lower coverage. The results are longer, and therefore, fewer contigs. Once the consensus maps are created they are aligned with an in silico reference sample and SV calls are made and presented in easy to read reports and graphs.


Improved – Our algorithms improve results by using more of the available data to build more accurate consensus maps and make more SV calls.

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

Fast – because HCE 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 hours 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 – In addition to the benefits of the cloud, which removes the need for expensive hardware and network configuration, the speed that’s gained from high-performance cloud computing (HPC) keeps the costs down allowing Hitachi to offer HCE at a low predictable fixed rate.


We have nicknamed HCE SV analysis pipeline the “Monkeypod Tree Process” after a famous monkeypod tree found in Oahu that has been used by Hitachi to symbolize comprehensiveness and wide range, both qualities which are embodied in HCE, since 1973.

It could be mistakenly assumed that the Monkeypod Tree Process could take a few days of processing time. However, one of the advantages of HCE is that our pipeline is optimized to decrease the computational requirements resulting in decreased analysis time. To further decrease analysis time HCE exploits high-performance cloud computing (HPC). HPC allows HCE to enlist and distribute the analysis process across many worker nodes. HCE has also been optimized for the lowest possible network latency. These factors combined with tightly coupled concurrent processing, means assembly, SV calling and reporting are completed up to 20x faster than other analysis methods with no loss in data. In fact, HCE often finds SV undetected by other methods.