Developer Spotlight: A De Novo Assembler Named Ray

sebastien boisvertWe recently launched the DNAnexus developer program, and to our delight one user was able to contribute a valuable new app in less than a day. Sébastien Boisvert, a doctoral student at the Université Laval in Québec, Canada, converted a software application he had previously written for short-read de novo assembly to an app for the DNAnexus community.

Boisvert is the mind behind Ray, a scalable genome assembler built specifically for next-gen, short-read sequence data and related applications, such as metagenomics. Ray was first reported in 2010 in the Journal of Computational Biology. Written in C++, it is an MPI-based parallel tool using a single executable to eliminate the need for writing perl scripts. Ray is sequencing platform-agnostic, so it can be used with data from any short-read sequencer.

Today, Ray is primarily used by bioinformaticians who have ongoing access to a supercomputer. The software’s peer-to-peer design makes it ideal to run on systems with hundreds or thousands of nodes — which also makes it just right for a cloud computing environment. When Boisvert heard that DNAnexus was opening its doors to developer-contributed apps, he immediately looked into how to submit Ray so even more users could have access to the tool. From his perspective, cloud computing offers a more instantaneous experience with massively parallel computing to people who don’t readily have supercomputer access, and also provides the type of infrastructure management that allows users to focus on what they want to compute, rather than how to manage queries and coding.

Boisvert remarked that the DNAnexus documentation for contributing an app was straightforward and that the interface in particular was easy to use. Writing the wrapper to convert the software code into an app took less than a day. He worked with the Developer Program support team at DNAnexus to make sure everything was working properly, and now Ray is available for any DNAnexus user to add to an analysis pipeline — and it’s free. (Check out Boisvert’s own blog about cloud computing options, where he notes that it’s fun to start an app in DNAnexus!)

As our developer program continues to grow, we look forward to working with more contributors to get their great apps into our platform so they can be broadly available to our growing community of users. If you’re interested in learning more about our Developer Program, please visit https://dnanexus.com/developers.