With the introduction of HiSeq X Control Software v3.1, the following library prep methods are supported on the HiSeq X:
HiSeq X Control Software v3.3—The control software interface guides you through the steps to load the flow cell and reagents before beginning a sequencing run. During the run, the software provides run metrics as they are generated.
To download software for the HiSeq X, see the HiSeq X Downloads.
Real-Time Analysis 2—The HiSeq X uses a new implementation of Real-Time Analysis (RTA) called RTA v2, which includes important architecture differences from RTA used on other Illumina sequencers.
For more information see the HiSeq X User Guide.
HiSeq Analysis Software v2.0 offers a fast, accurate solution to high-throughput WGS, processing data up to 8x faster than existing analysis methods. HiSeq Analysis Software v2.0 uses the proven Isaac workflow to provide a full spectrum of variant types, including single nucleotide variants (SNVs), indels, structural variants (SVs), and copy number variants (CNVs) from BCL file inputs. HiSeq Analysis Software v2.0 can be installed and run on commodity hardware using the CentOS 6 operating system. See the HiSeq Analysis Software v2.0 support page for more information.
The HiSeq X Control Software features an option to send run and health data to BaseSpace, the Illumina cloud computing environment. With this feature enabled, you can monitor run metrics from any location in a web browser. See the HiSeq X Ten Lab Setup and Site Prep Guide for BaseSpace network considerations.
If you do not choose to use HiSeq Analysis Software v2.0 on premises, or to connect to BaseSpace, use the bcl2fastq2 conversion software to convert HiSeq X BCL file output to standard FASTQ file formats for downstream analysis using third-party analysis solutions.