Illumina Basespace Genomics: Lifting the Burdens in Bioinformatics

Greg Bates, November 19th, 2012

Illumina BaseSpaceThe Illumina Basepace API is a key stepping stone to simplifying genomics software development by third parties with a platform as a service. The API allows you to build for any platform, web, desktop, or “Native apps.” Illumina offers whole-genome sequencing, individual genome sequencing, and with Basespace offers processing, storage and apps sold by third party vendors.

Monya Baker pointed out in her nature blog that Basespace is partially aimed at becoming a crowd-sourced evaluator of bioinformatics code:

“Illumina, for its part, is trying to remove everything that’s burdensome about bioinformatics, says Jordan Stockton, marketing director of computational biology. This week the company is launching applications in BaseSpace. Illumina’s instruments will upload raw sequencing reads to the cloud, where a bevy of apps await. These perform alignment, annotation and more. Illumina announced products from nine partner companies this week and will also let budding bioinformaticians put their own creations in BaseSpace as well, a possibility that should help the scientific community test out new code – in an environment built to support data from Illumina’s instruments.

Besides giving Illumina customers more bioinformatics tools to play with, BaseSpace should start to generate its own revenue stream. Starting in 2013, the company will keep a cut of any fees collected by application providers. Until then, though, BaseSpace and all its applications are free.”

The end point of collecting and analyzing all this data is improving human health. Among its disease targets are cancer and cystic fibrosis. Using cytogenetics, illumina aims to detect abnormalities, including amplifications, deletions and rearrangements  in chromosomes across the genome.

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