Quick Start

Start the pipeline with the DRAGEN_Solid_WGS_TO-4.4.4.sh Bash script. The script is installed in the /usr/local/bin directory. The Bash script is executed on the command line and runs the software with Docker (or Apptainer if specified).

For arguments, refer to Command-Line Options. You can start from BCL files or from the FASTQ folder produced by BCL Convert. The following requirements apply for both methods:

• Path to the sequencing run or FASTQ folder. Copy the run or FASTQ folder to the DRAGEN server into the staging folder with the following recommended organization: /staging/runs/{RunID}. You can copy the run folder onto the DRAGEN server using Linux commands such as rsync. The sample sheet within the run folder is used unless otherwise specified through the command line.

• Run folder must be intact. Refer to Starting from BCL Files for input requirements.

• If the analysis output folder path is different from the default, provide the analysis output folder path. Refer to Command-Line Options.

Before running the analysis, confirm that the output directory for the software to write to is empty and does not include results of previous analyses.

Storage Requirements

For optimal performance, run analysis on data stored locally on the DRAGEN server. Analysis of data stored on NAS can take longer and performance can be less reliable.

The DRAGEN server provides an NVMe SSD in the /staging directory to use as the software output directory. Network-attached storage is required for long-term storage.

When running the pipeline, use the default settings or set the -analysisFolder command line option to a directory in /staging to make sure the DRAGEN server processes read and write data on the NVMe SSD.

Before beginning analysis, develop a strategy to copy data from the DRAGEN server to a network‑attached storage. Delete output data on the DRAGEN server as soon as possible.

The following are the run and analysis output sizes for each sequencing system per 101 bp:

Sequencing System	Run Folder Output (Gb)	Analysis Output (Gb)	Minimum Disk Space (Gb)
NextSeq 500/550/550Dx (RUO) HO flow cell	32-55	82-85	150
NovaSeq 6000/6000Dx (RUO) SP Flow Cell	85-100	250-374	300
NovaSeq 6000/6000Dx (RUO) S1 Flow Cell	164-200	360-665	800
NovaSeq 6000/6000Dx (RUO) S2 Flow Cell	290-460	890-1600	1500
NovaSeq 6000/6000Dx (RUO) S4 Flow Cell	800-1200	2700-4100	3000
NovaSeq X 1.5B	213	352	800
NovaSeq X 10B	1100	1800	3000
NovaSeq X 25B	1800	3300	4000
NextSeq 1000/2000	41	107	150

When launching the analysis, the software checks that the minimum disk space required is available. If the minimum disk space is not available, the software shows an error message and prevents analysis from starting. If disk space is exhausted during a run, the run shows an error and stops analyzing.

Moving or modifying files during an analysis may cause the analysis to fail or provide incorrect results.