HiSeq Analysis Software v2.1 is a software package for processing sequencing results generated by Illumina HiSeq X sequencing systems. HiSeq Analysis Software performs analysis on the base calls and quality scores generated by the Real-Time Analysis (RTA) software. During the sequencing run, HiSeq Analysis Software produces information about alignment, variants, or other analysis results for each sample in an analysis. HiSeq Analysis Software can also be used to compare a tumor-normal sample pair, and will identify variants specific to the tumor sample.
For all analysis types, the analysis is run with a simple command line. Each workflow includes recommended default settings for the available options, which are specified in the sample sheet.
HiSeq Analysis Software v2.1 supports a multi-step analysis workflow that is amenable to scripting.