NovaSeq X Run Planning - BCL Convert

Log in to BaseSpace (BSSH)

Navigate to either the BSSH private domain or Illumina's public BSSH domain. Sign in with the appropriate credentials.

1. Access the appropriate workgroup to plan the sequencing run

2. Select "Runs" from the top panel

3. Select "New Run"

4. Select "Run Planning" from the right-hand dropdown

Specify Run Settings

1. Name the run

2. For Instrument Platform, select "NovaSeq X Series"

3. For Secondary Analysis, select "BaseSpace / Illumina Connected Analytics"

4. For Read Lengths:

   1. Read 1: 151

   2. Index 1: 10

   3. Index 2: 10

   4. Read 2: 151

5. Select "Next"

6. For Application, the recommendation is to use the latest version, but the product is compatible with all versions of DRAGEN BCL Convert.

1. For Library Prep Kit, select either "Illumina 5-Base DNA Prep" or "Illumina 5-Base DNA Prep with Enrichment"

2. For Index Adapter Kit, select the appropriate kit from the available options ("Illumina DNA-RNA UD Indexes, Set X Tagmentation" where X is the appropriate plate version; if pooling indexes from multiple plates, select "A B C D" version)\

   
3. Select "Next"

4. Leave the following fields as default:

   1. Adapter Read 1

   2. Adapter Read 2

   3. Override Cycles

   4. WARNING: Trimming is critical for analysis. Changing these values can result in reduced methylation calling accuracy.

1. In the sample table, fill in specific sample information for Sample ID, Well Position, and Project

   1. I7 index, Index 1, I5 index, and Index 2 should fill in automatically based on selected Well Position

   2. Note: Leave Barcode Mismatches Index 1 and Barcode Mismatches Index 2 as their default values

1. Select "Next"

2. Review the Planned Run Details page

1. Add another configuration if desired

2. Select one of the following options:

   1. Select "Export" to export the SampleSheet.csv file

   2. Select "Save as Planned" to save the planned run