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CosmosID Adds Cloud Option with the Release of Metagenomics App on Illumina's BaseSpace


NEW YORK (GenomeWeb) – Bioinformatics firm CosmosID has released a new app on Illumina's BaseSpace Apps store that provides some of the capabilities of its Genome Identification Universal System (GENIUS) metagenomics analysis software and database.

The app adds a cloud-based option to the company's existing portfolio, which includes a service offering and an appliance installation, and also provides an initial exposure to the company's full services and capabilities that will hopefully encourage new customers to try out its more detailed solutions, Michael Moritz, the company's chief operating officer, told GenomeWeb.

CosmosID's GENIUS couples internally developed algorithms with company curated databases of information on bacteria, viruses, molds, and fungi. Customers use the solution to analyze data from shotgun sequencing experiments and identify microorganisms present in metagenomics samples collected in hospitals and clinical laboratories. The company's main algorithm, NmerCE, uses a kmer-based approach to match data from input samples to its reference database and to categorize them by species, subspecies, and strain. The solution is able to discriminate between pathogens from closely related species even at low concentrations without requiring prior knowledge of the diversity, complexity, or community composition of the sample.

Like the broader application, the GENIUS app uses CosmosID's reference database of microbial information —called GeneBook — and NmerCE, to process metagenomic reads, but it only uses a subset of the bacterial information contained in GeneBook, Kelly Moffat, the company's director of product management and a senior bioinformatics engineer, told GenomeWeb. The full database contains data from about 22,000 strains and the app only has access to about 4,800. The app also does not have access to some of the customized algorithms and specialized databases, initially developed to meet specific customer needs, that are also available in the broader offering, she said.

To use the BaseSpace app, researchers can upload their sequencing reads directly from an Illumina sequencer, their local storage, or the National Center for Biotechnology Information's Sequence Read Archive to the cloud and then run the GENIUS app. After the analysis is completed, the tool generates a table of results including the organism name, any substrains found in the sample, the taxonomies of the bacteria, frequency information, information on virulence factors, and relative abundances. They can also view an interactive pie chart that lets users home in on bacterial groups of interest within their samples, explore the breakdown of the taxonomic groups, and so on. Later iterations of the app might include additional visualization capabilities, Moffat said.

CosmosID is offering customers a chance to try out the new BaseSpace app at no cost up until April 15, Moritz said. The company has made available some sample Fasta files in the cloud for customers who want to test the solution before moving their data in.

CosmosID charges between $200 and $550 per sample. The exact price depends on several factors — such as the customer's existing relationship with the company or an existing license — but it is primarily volume-based, Moritz said.

Those prices apply no matter what version of the company's solution customers use. In addition to the new cloud option, GENIUS is also available as an appliance installed locally at a client's site. For the appliance, the company offers packages that can include per-sample pricing all the way up to an all-you-can-use license that can last for a few months or longer, Moritz said. The company also offers a "virtual lab" option that provides a full service to customers from sample all the way through to the final report.

In addition to launching the BaseSpace app, ComosID is also expanding its main GENIUS offering. The company plans to add additional information to GeneBook this year including a new parasite database that will come out in the second or third quarter, Moritz said, and it will also release data on antibiotic resistance genes. The company is also adding more strains to its bacterial database, bringing the number of strains up from 22,000 to 30,000 bacteria in total.

CosmosID competes with a number of other companies that are also developing informatics solutions for the space. That list includes One Codex, which is working on commercializing a platform of the same name that is currently in beta, for identifying microbial pathogens from NGS data and can return results in a matter of minutes, according to the firm. Reference Genomics won an award from the US Centers for Disease Control and Prevention for one application of its technology: strain-typing Shiga toxin-producing Escherichia coli. Meanwhile, Aperiomics offers three kinds of sequencing and bioinformatics-based pathogen detection services for identifying both known and unknown pathogens as well as characterizing all microorganisms found in a single sample. 

Some institutions have also developed internal solutions. Researchers at Boston University School of Medicine and George Washington University, for instance, developed Pathoscope, statistical software that's designed to distinguish between closely related pathogenic species and strains in genomic data from infected tissues. Meanwhile, researchers at the University of California, San Francisco and elsewhere developed the sequence-based ultrarapid pathogen identification (SURPI) pipeline, which runs on both cloud and local infrastructure. 

However, Moffat believes that CosmosID's internally curated database sets it apart from its competitors. "We've spent years curating the database so that we have the strains of significance ... that are cleaned up [and] don't have a lot of the contamination that you see [with public resources]," she said. She also noted that some other solutions were initially developed for research and academic use and then repurposed for clinical contexts. CosmosID's solutions, on the other hand were developed with the clinical market in mind, and as such the system has been honed to ensure that it provides quality results and avoids false positives.