BEAR Applications

sequenza 3.0.0-foss-2021b

Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.

Accessing sequenza 3.0.0-foss-2021b

To load the module for sequenza 3.0.0-foss-2021b please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load bear-apps/2021b
module load sequenza/3.0.0-foss-2021b

BEAR Apps Version

2021b

Architectures

EL8-cascadelake — EL8-haswell — EL8-icelake — Ubuntu20.04-haswell

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.

Extensions

• copynumber 1.36.0
• iotools-0.3-2
• seqminer 8.4
• sequenza 3.0.0
• squash 1.0.9

More Information

For more information visit the sequenza website.

Dependencies

This version of sequenza has a direct dependency on: foss/2021b Pandoc/2.13 R/4.2.0-foss-2021b R-bundle-Bioconductor/3.15-foss-2021b-R-4.2.0

Required By

This version of sequenza is a direct dependent of: sequenza-utils/3.0.0-foss-2021b

Other Versions

These versions of sequenza 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.

Last modified on 10th August 2022