How to configure the NextSeq 550 for BeadArray Scanning

Scanning CytoSNP, MethylationEPIC, or Karyomap* BeadChips on the NextSeq 550 requires configuring the settings in the NextSeq Control Software (NCS):

1. Open the NCS

2. From the NCS Home Screen navigate to Manage Instrument → System Configuration → BeadChip Scan Configuration (Figure 1)

3. In the BeadChip Scan Configuration, complete the required fields (Figure 2):

• dMap Location: Browse to the location where the dMaps for the BeadChips are stored

• Output Location: Browse to the location where the BeadChip scan folder will be stored

• Saved Image Type: Select among jpeg,png and tiff

• Output File Type: two options, gtc only, gtc and idat Note: default is gtc only, it is recommended to select gtc and idat.gtcs are required for analysis of CytoSNP-850K in BlueFuse Multi. MethylationEPIC BeadChips will only generate idat files as they are not for genotyping.

1. Click Save to proceed to the next screen for Scan File Configuration (Figure 3)

• The BeadChips that can be scanned on the NextSeq 550 will be listed on this screen. If the beadchip of your interest is not in the list please check with illumina Technical Support

• For each BeadChip type and version, browse to the location of the Manifest and Cluster file

• Once completed, click Save

Figure 1: Navigating to the BeadChip Scan Configuration Settings on the NextSeq 550

Figure 2: Setting the BeadChip Scan Configurations on the NextSeq 550

Figure 3: Scan File Configuration on the NextSeq 550

Note: For further reference, consult the Scan Setup section from the NextSeq 550 Sequencing System Guide. *Karyomap v2 BeadChips are sold and supported by Vitrolife

Additional information: Which Infinium BeadChip types can be scanned using the NextSeq 550?

For any feedback or questions regarding this article (Illumina Knowledge Article #5236), contact Illumina Technical Support [e-mail].