We are discontinuing development of HiSeq Analysis Software v0.9. The software will continue to be available for download. However, we recommend transitioning to newer, more cutting edge solutions for your analysis.
As a replacement for HiSeq Analysis Software v0.9, we recommend using the Isaac Enrichment and Isaac Whole Genome Sequencing apps available on BaseSpace and BaseSpace Onsite. In addition, bcl2fastq Conversion Software is available to demultiplex and convert BCL files to FASTQ files on your local computer hardware. BaseSpace and BaseSpace Onsite offer fully supported software solutions, and, along with bcl2fastq, are continuously optimized through ongoing development efforts.
HiSeq Analysis Software provides rapid and easy alignment and variant calling for Whole Human Genomes or libraries prepared with the Nextera Rapid Capture (NRC) exome enrichment kit. For Whole Human Genome Sequencing, HiSeq Analysis Software features the Isaac analysis workflow, which is the fastest accurate sequence analysis software, providing a 4-6 times speed increase over existing methods. For NRC analysis, the BWA alignment and GATK variant calling methods are used. The software can be run through the command line or through a Graphical user interface called Analysis Visual Controller Software (AVC). More details on the supported workflows: