NextSeq 500 FAQs

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  • Software


  • Local Run Manager run mode - No sample sheet is required.

    Manual run mode - A sample sheet is required in the following cases:

    • The system is configured for Run Monitoring and Storage in BaseSpace Sequence Hub. 
    • When you use converted FASTQ files with a third-party analysis software. Use the Local Run Manager GenerateFASTQ software module to create a sample sheet. 

    For NCS 2.2 or earlier, a sample sheet is only required when in standalone mode with converted FASTQ files and a third-party analysis software. Use Illumina Experiment Manager to create a sample sheet.

  • Analysis


  • If data transfer is interrupted during a run, data are stored temporarily on the instrument computer until the connection is restored. When the connection is restored, transferring of data resumes automatically.

    If the connection is not restored before the end of the run, data must be removed from the instrument computer manually before a subsequent run can begin.

    NextSeq 550 Systems running NCS v4 or later can use Local Run Manager software modules for on-instrument analysis. 

    Additional analysis tools are available on BaseSpace Sequence Hub. You can also configure the NextSeq System to transfer data to a local server and perform analysis using third-party software.