We are humbled and excited by the overwhelming attention BaseSpace, BaseSpace Onsite, and the BaseSpace Core Apps have received at AGBT. Things were set in motion on Wednesday by a review of the BaseSpace RNA-Seq Apps (TopHat and Cufflinks) by James Hadfield from Cancer Research UK as a part of his presentation at the Illumina User Meeting. Then on Thursday, during the standing-room only Illumina Workshop, our own Gary Schroth gave a “User’s Perspective” talk on RNA-Seq right after Sheila Fisher’s hot-off-the press presentation of HiSeq X10 and NextSeq datasets from the Broad Institute. Gary gave a deep dive of the TopHat and Cufflinks Apps on BaseSpace. Gary emphasized the high usability and the end-to-end workflow now enabled by BaseSpace. The workflow starts with creation of samples, libraries and runs for the NextSeq on the Prep tab, followed by real-time monitoring of sequencing metrics, and finally the streamlined analysis of data resulting in graphical interactive plots of expression profiles. Gary also mentioned that he is not a bioinformatician, but can now perform RNASeq analysis all by himself.
On Thursday evening, the first-ever AGBT “Electronic Poster Session” was held, where about 30 software vendors showcased their solutions in a large, well-catered room (chocolate fountain, crabs, sushi and all). The two of us who were demo-ing BaseSpace were kept busy throughout the two hours and we definitely got the sense that the value proposition of the BaseSpace platform and Apps resonated with all users who stopped by our booth.
Finally, we would like to respond to some questions that have come up in the twitter-verse based on the James Hadfield and Gary Schroth presentations:
1. To cite BaseSpace in journal manuscripts: we recommend citing the specific URL as appropriate
- To cite BaseSpace in general: basespace.illumina.com
- To cite a particular App: https://basespace.illumina.com/apps/303303/BWA-Enrichment etc. (Each App has a dedicated “App description page” that is accessible from the App tab on the top menu bar)
- To cite algorithms/methods used in the Apps: All the methods used within apps are referenced within the corresponding App description page
- To cite a particular Project, with embedded datasets and App analysis sessions, again use the particular URL associated with the dataset. Here is an example of a publicly shared Nextera Rapid Capture Exome project, with 12 exome samples run on the HiSeq 2500 (you will notice the associated “Analyses” and “Samples” along the tab on the left) : https://basespace.illumina.com/projects/3289289/
2. Timing of availability of the BaseSpace Core Apps: The BWA/GATK whole-genome (WGS) App, the BWA/GATK Exome (Enrichment) App, as well as the Strelka-based Tumor-Normal App are available on BaseSpace today. The Isaac-based WGS and exome Apps, along with the RNA-Seq Apps will be available by the end of February.