HomeCLC FAQ - Basics: Installation, data, system resourcesSystem and resourcesAre the tools of the CLC Workbenches or Servers multi-threaded?

3.2. Are the tools of the CLC Workbenches or Servers multi-threaded?

A list of analyses offered by the Genomics Workbench, Biomedical Genomics Workbench or the Genomics Server that benefit from the availability of multiple cores can be found on this page of our manual:


The tools listed are those that could benefit from running on computers with multiple CPU cores, but this does not mean that they use all CPU cores available the whole time.

For the CLC Main Workbench, the only analyses that make use of multiple cores are the 'Create Alignment' tool and 'BLAST'.

While Workbenches can be run on systems with just one core, your experience will generally be much better on a machine with at least 2 cores. This can make a difference for running analyses, but will also make a difference when it comes to viewing large or complex datasets, such as read mappings or alignments.

The following pages of our manual may also be of interest:

Restricting the number of cores that the Genomics Workbench analyses can use:

Restricting the number of cores that the Genomics Server can use:

Please note that some analyses include a native binary phase, and the binary phases of these tasks are not currently affected by such restrictions you put on the java process. Analyses with a native binary phase are:

  • De novo assembly
  • Read mapping
  • RNA-seq
  • Extract and counting tags for small RNA analysis and Expression Profiling by tags
  • Blast searches*

*BLAST is an exception in that we use the NCBI binaries directly. Here, the maximum number of threads used by a local BLAST search is configurable via the Wizard for any given job.

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