Running Velvet from the Workbench
To run Velvet, open a Workbench with the External Applications Client Plugin installed. Then:
- Go to:
Toolbox | External Applications (
) | CLC bio Velvet (
)
- Confirm where you wish to run the job.
- Select (
) the reads to assemble and configure the Velvet parameters, as shown in figure 12.14.
Figure 12.14: Configuring Velvet parameters from a Workbench. - Click on the button labeled Next.
- Specify where to save the results.
- Click on the button labeled Finish.
The process that follows has four steps:
- The sequencing reads are exported by the server to a FASTA file. The FASTA file is a temporary file that will be deleted when the process is done.
- The velvet script is executed using this FASTA file and the user-specified parameters as input.
- The resulting output file is imported into the save location specified in the save step of the Workbench dialog, and the user is notified that the process is done.
- All temporary files are deleted