NovaSeq X Run Planning - BCL Convert

This page gives an overview of generating a Sample Sheet on BaseSpace for sequencing on NovaSeq X Sequencing Systems. This Sample Sheet is required for on-prem BCL Convert via DRAGEN Server.

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: 0

   3. Index 2: 0

   4. Read 2: 151

5. Select "Next"

6. For Application, select "DRAGEN BCL Convert - 4.4.10"

1. For Library Prep Kit, select either "Illumina TruPath Genome (C2)" or "Illumina TruPath Genome (C8)"

2. For Index Adapter Kit, select "Not Applicable"

   
3. Select "Next"

4. Leave the following fields as default:

   1. Adapter Read 1

   2. Adapter Read 2

   3. Override Cycles

5. In the sample table, fill in specific sample information for Sample ID and Project. Note that Sample ID's must be unique.

Illumina TruPath Genome flow cells support one sample per lane. For the C2 flow cell, enter samples information up to two samples. For the C8 flow cell, enter information for up to eight samples.

1. For analysis settings, select "No" for Combine sample FASTQs across lanes.

   
2. For auto-detect demux mode, select "None"

1. For auto-detect minimum number select "Auto (default)"

1. Review the Planned Run Details Page:

   
2. Add another configuration if desired.

3. Select "Export" to export the SampleSheet.csv file. Attach the Sample Sheet to the Sequencing Run during the run setup workflow for performing a manual run on the NovaSeq X. The Sample Sheet will be copied to the sequencing run output folder, where it may be used for DRAGEN BCL Convert via on-prem server.