Set up a Run

1.

Select the Runs tab, and then select New Run.

2.

Select NextSeq 1000/2000.

3.

In the Run Name field, enter a unique name of your preference to identify the current run.

The run name can contain alphanumeric characters, spaces, dashes, and underscores.

4.

Select one of the following analysis locations.

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BaseSpace Sequence Hub—Analyze sequencing data in the cloud.

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Local—Analyze sequencing data on-instrument.

5.

Select an analysis type and version.

6.

Select the following instrument settings. Depending on the library prep kit, recommended options are automatically selected. Some library prep kits have hard-coded number of indexes reads and read types, which cannot be changed.

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Illumina library prep kit

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Index adapter kit

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Number of index reads

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Read type

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Number of sequencing cycles per read

7.

Enter sample information into the Sample Data spreadsheet using one of the following options. To group samples for data aggregation during downstream analysis, assign a name for the group in the Group column.

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Paste sample IDs and either index plate well positions or i7 and i5 indexes directly from an external file. Before pasting, enter the number of sample rows in the Rows field, and then select+.

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Select Import Data, and then select your sample sheet. Make sure the index sequences specified in the BCLConvert_Data sample sheet section match the index kit selected in the Instrument and that your sample sheet is in v2 format.. Altering your sample sheet after initial download can result in analysis failure.

•

Manually enter sample IDs and corresponding well positions or indexes. If Not Specified is selected for the library prep kit, enter Index 2 sequences in the forward orientation.

8.

Select Next.