The GeoMx NGS Pipeline uses a series of novel algorithms to process sequencing files from FASTQ to the Digital Count Conversion (DCC) file format that is read by the DSP instrument for further analysis

Accessing GeoMxNGSPipeline

To load the module for GeoMxNGSPipeline please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load bear-apps/2021b
module load GeoMxNGSPipeline/

BEAR Apps Version




The listed architectures consist of two part: OS-CPU.

  • BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
  • BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.

More Information

For more information visit the GeoMxNGSPipeline website.

Other Versions

These versions of GeoMxNGSPipeline are available on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Version BEAR Apps Version
2.2 2020a
2.0 2019b

Last modified on 23rd January 2023