Output Folder Structure

By default, the NovaSeq X Series generates output files in the output folder selected in the external storage settings.

At a high level, the outputs are organized in the following structure:

/usr/local/illumina/runs/<run_id>/

Analysis (secondary analysis files)

Data (primary analysis BCL files)

InstrumentAnalyticsLogs

InterOp

Logs

RTA.cfg

RTAComplete.txt

CopyComplete.txt

RunCompletionStatus.xml

RunInfo.xml

RunParameters.xml

SampleSheet.csv

In addition to generating files specific to each application, DRAGEN provides metrics from the analysis on a per sample basis and in aggregated reports. Depending on the modes of operation, there might be additional metric files included in the output. For more information on the different levels of the reports, refer to NovaSeq X Series Secondary Analysis Reports.

For more information on DRAGEN secondary analysis output files and metrics, refer to the Illumina DRAGEN Bio-IT Platform support site page.