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New Release of the iPlant Discovery Environment
The second quarter (Q2) release of the iPlant Collaborative’s Discovery Environment provides new functionality for analyzing ultra high throughput sequence (UHTS) data from both Illumina and AB SOLiD sequencing machines. It also launches a new look and feel for iPlant's user interface. The three new scientific workflows enable users to:
- Pre-process UHTS sequence data,
- Determine transcript abundance (RNAseq), and
- Perform variant detection analysis.
The FASTX toolkit is used for sequence datasets needing pre-processing. For transcript abundance analyses, Bowtie and TopHat perform the sequence alignment to a reference sequence and Cufflinks is used to quantify transcript abundance. For variant detection, alignment is performed using the Burrows-Wheeler Aligner (BWA) and variant calling is implemented using SAMtools. The Q2 release allows sequence alignment and single-nucleotide polymorphism (SNP) detection against the Arabidopsis thaliana v9 and Zea mays B73 v2 genomes. Additional plant genomes will be supported in future releases. A graphical user interface readily allows all researchers to analyze UHTS data. Additional information about the tools in iPlant’s Discovery Environment is available online.
The Q2 release provides a working demonstration of several new iPlant cyberinfrastructure features that underlie the scientific workflows. The architectural framework now supports:
- Importing data from external repositories via a URL,
- A metadata-driven specification of graphical user interfaces for bioinformatics tools in the Discovery Environment, which, in the future, will allow tool contributors to create flexible user interfaces for tools they wish to incorporate into the Discovery Environment,
- Job processing in a cluster environment to provide all scientists access to multiple-processor grid computing for increased computing performance, and
- Storing data in an IRODS infrastructure providing efficient storage and archiving of large datasets, and which will, in a future release,
allow for sharing of datasets.
Users can request accounts immediately using the form below. Access will be provided on a rolling basis.