File paths for the NextSeq 500/550

The run folders on the NextSeq 500/550 include run data, along with many files that are helpful for reviewing run performance and troubleshooting, if necessary.

NextSeq Control Software (NCS) 2.2.x and 4.0.x Run Folder: The file path of each run folder is:

  • D:\Illumina\NextSeq Control Software Temp[Run_Folder]

Key files in this location include:

  • Runinfo.xml

  • Runparameters.xml

  • InterOp folder

  • Thumbnail Images

  • SampleSheet.csv

  • Cycle Logs:

    • (D:\Illumina\ NextSeq Control Software Temp [Run_Folder]\Logs)

  • Diagnostic.00.log:

    • (D:\Illumina\ NextSeq Control Software Temp [Run_Folder]\Logs)

  • Focus Images:

    • (D:\Illumina\ NextSeq Control Software Temp[Run_Folder]\Images\Focus\L00X\C1.1)

  • RTA Logs:

    • (D:\Illumina\ NextSeq Control Software Temp[Run_Folder]\RTALogs)

  • RTA Config:

    • (D:\Illumina\ NextSeq Control Software Temp[Run_Folder]\Data\Intensities\RTAConfiguration.xml)

  • FirmwareVersions.txt:

    • (D:\Illumina\ NextSeq Control Software Temp[Run_Folder]\Config)

  • DemultiplexSummaryF1L1.txt

    • (Generated after FASTQ generation completes): [run folder]\Alignment_#[date and time folder]

BCL Files (raw data output from sequencing) are saved in 2 locations:

  • D:\Illumina\NextSeq Control Software Temp[Run Folder]\Data\Intensities\Basecalls

  • [Output Folder][Run Folder]\Data\Intensities\Basecalls

Additional helpful file paths:

  • NCS Logs in Windows 7: (C:\Illumina\NextSeq Control Software\Logs)

  • NCS Logs in Windows 10: (D:\Illumina\NextSeq Control Software\Logs)

  • Maintenance Logs: (D:\Illumina Maintenance Logs)

  • Preventative Maintenance (PM): D:\Illumina\PreventativeMaintenance

  • NextSeq Control Software Config: (C:\ProgramData\Illumina\NextSeq Control Software\InstrumentShell.NextSeqControlSoftware.Options.cfg)

  • BaseSpace Broker Logs: D:\Illumina\BaseSpace broker (NCS 2.2.x only)

  • Restart Universal Copy Service (UCS): (C:\ProgramFiles\Illumina\UniversalCopyService\ucs.exe) (NCS 4.0.x only)

  • System Check Results (all): D:\Illumina\SystemCheckResults

Beadarray folder: (The NextSeq 550 can be used to scan select beadarrays.)

  • [Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\Config folder

  • [Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\Focus folder

  • [Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\Logs folder

  • [Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\GTC files

  • [Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\IDAT files

  • [Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode]\Image files

  • [Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode][Barcode]_sample_metrics.csv

  • [Date]_[Instrument Name]_[Scan#]_[Barcode][Barcode][Barcode]_section_metrics.csv

  • [Date]_[Instrument Name]_[Scan#]_[Barcode]\ScanrParameters.xml

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