New Single-Cell Genomic Studies Demonstrate Utility of SPAdes Assembler

spades de novo assemblerThis summer we saw some new publications underscoring the need for a high-quality assembler for single-cell genomic sequencing projects — particularly in clinical settings.

Two papers demonstrate this well, and both use the assembler SPAdes to perform needed assemblies. (SPAdes, which can be used for both standard isolates and for single-cell MDA bacterial assemblies, is available as an app through the DNAnexus platform.)

“Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum” came out in PNAS in June, and “Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform” was published in Genome Research in May. Both papers come from the J. Craig Venter Institute and highlight the critical need for single-cell genomics to characterize organisms that cannot be cultured with traditional methods.

“Single-cell genomics is becoming an accepted method to capture novel genomes, primarily in the marine and soil environments,” the scientists write in Genome Research. “Here we show for the first time that it also enables comparative genomic analysis of strain variation in a pathogen captured from complex biofilm samples in a healthcare facility.”

One of the key limitations to performing single-cell genomics has been that most assemblers are not optimized to handle this type of data. Lack of uniformity in read coverage and increased numbers of chimeric reads and sequencing errors are common problems in single-cell work.

SPAdes, developed by researchers at the St. Petersburg Academic University Algorithmic Biology Laboratory in collaboration with Pavel Pevzner at the University of California, San Diego, fills this niche. The assembly tool, which was recognized as a top performing assembler in the GAGE-B Evaluation, generates single-cell assemblies, providing far more information about microbial genomes from metagenomic studies than traditional assemblers. SPAdes can be used with standard isolates as well as single-cell bacteria assemblies.

SPAdes has been ported to DNAnexus and is available as an app to any user of the new platform. Input for the app is a set of reads in FASTQ format. In SPAdes 2.5, the user can specify multiple libraries, which all will be used for repeat resolution and gap closing. SPAdes does not yet have a scaffolder, so in the case of mate pair sequence data, using an external scaffolder is recommended. You can check out the app by logging in to DNAnexus and searching the app library for SPAdes.

Developer Spotlight: A De Novo Assembler Named Ray

We 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.