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Illumina Updates BaseSpace Onsite With Better Instrument Support, More Apps


NEW YORK (GenomeWeb) – Illumina has launched a new version of BaseSpace Onsite, a locally installable version of the BaseSpace cloud that provides a subset of the capabilities that are available on the larger infrastructure including applications for analyzing whole-genome or exome sequence, tumor-normal data, transcript assembly, expression profiling, and variant analysis .

Illumina launched BaseSpace Onsite in 2013 to provide an on-premises alternative for customers of the company's sequencers who for various reasons are unable to use remote infrastructure to analyze their data. It's also a gentler introduction to the cloud for customers who are interested in cloud infrastructure but aren't quite yet ready to make the jump, Brady Davis, senior director of Illumina's enterprise informatics business, said this week. BaseSpace Onsite provides a way for these clients to reap some of same storage benefits and access some of the analytical capabilities that are available to the customers of the BaseSpace cloud from the safety of their firewalls.

Version 2.0, which launches this week following a beta that began in April and wrapped last month, builds on its predecessor and incorporates valuable new features based on customer feedback. Its features include support for customers with multiple instruments — the system now accepts data streamed from both the HiSeq 2500 and the NextSeq 500 and there are plans to support additional sequencing instruments in future releases of the platform, Raymond Tecotzky, market manager for Illumina's informatics ecosystem, told GenomeWeb.

This release also doubles the number of apps that were available in the earlier system. There are now a total of 18 apps in the system including Illumina-developed apps for analyzing data from targeted amplicon sequencing and metagenomics data; and third party-developed apps for metagenomics data analysis, de novo assembly, custom enrichment, targeted exome sequencing, RNA-seq analysis, long reads, and phasing data. These apps were selected based on utilization trends observed on BaseSpace cloud as well as customer feedback, Davis said.

There are also upgrades to version 2.0 of BaseSpace Onsite that make it simpler and faster to incorporate updates made to BaseSpace cloud, Davis said. The new release also includes an importer tool that lets user upload previously generated individual sample, variant, and manifest data files up to 25 gigabytes in size; an improved search feature; and a new delete feature for clearing out old analysis runs and samples from projects to free up storage space. BaseSpace Onsite 2.0 offers short-term storage of up to 9 terabytes of genomic data and includes an archiving feature for longer-term storage.

BaseSpace Onsite retails for $60,000 for the first year and an additional $15,000 per year afterwards to cover software licensing fees. Illumina isn't disclosing how many systems it has placed at customer sites. However, Tecotzky said that a "significant percentage" of new instrument placements in contexts where cloud use is restricted by compliance, regulatory, or bandwidth requirements have also included installations of BaseSpace Onsite. The company is also not disclosing the identities of BaseSpace Onsite customers, but Tecotzky characterized them as smaller labs that are focused on clinical research projects.

Meanwhile, the company continues to make improvements to the BaseSpace cloud including connecting more sequencing instruments and improving existing connections between already aligned instruments and software platforms, according to Davis. Over the past year, the company has seen on average 10 percent growth in usage statistics per quarter, he said. In total, over 4,000 customer instruments have been linked to the BaseSpace cloud; and about 30,000 users have accessed and used applications on the cloud — the number of users is currently about 20 percent per quarter on average, Davis said. BaseSpace cloud has been used for over 260,000 analysis runs with an average growth rate of about 20 percent per quarter.

The BaseSpace cloud currently offers access to over 60 apps including 30 third-party tools developed through Illumina's native apps development program and the remainder internally developed apps created through the BaseSpace Core apps and the BaseSpace Labs apps programs, Tecotzky said.Apps are grouped into categories that make it easier for users to search them. Groupings include apps for ChIP-seq, differential expression, metagenomics, de novo assembly, gene fusion detection, methyl-seq, proteomics, quality, resequencing, RNA-seq, small RNA, synthetic long reads, targeted sequencing, tumor normal, and variant analysis.