# Run setup modes for the NextSeq 500/550 The NextSeq 500/550 run setup modes available depend on the version of the Windows operating system, and NextSeq Control Software (NCS) installed. (Terms: LRM = Local Run Manager / BSSH = BaseSpace Sequencing Hub) **Windows 7 with NCS v2.2 or lower\\**\* Standalone Mode * Set up the run in the control software. * BSSH is not used. The data output of the run is only bcls; use bcl2fastq for FASTQ generation. Prep Tab in BSSH * If using BSSH for analysis (FASTQ generation, etc.), the run must be planned in Prep Tab. \\\*LRM is not available on Windows 7-based systems. Toggle between modes in Control Software (Manage Instrument / System Configuration). **Windows 10 with NCS v4+ and LRM v2** LRM Mode * Create the run in LRM. * The run can also be sent to BSSH. Manual Mode * Set up the run in the control software. * A sample sheet is required if uploading the run to BSSH. Toggle between modes during run setup (after selecting Sequence). \ \ \
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