sequenza 3.0.0-foss-2021b-MScTools 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-MSc
To load the module for sequenza 3.0.0-foss-2021b-MSc 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-MSc
BEAR Apps Version
EL8-cascadelake — EL8-haswell — EL8-icelake
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.
- copynumber 1.38.0
- seqminer 8.4
- sequenza 3.0.0
- squash 1.0.9
For more information visit the sequenza website.
This version of sequenza has a direct dependency on: foss/2021b Pandoc/2.13 R/4.2.0-foss-2021b R-bundle-Bioconductor/3.16-foss-2021b-R-4.2.0
This version of sequenza is a direct dependent of: sequenza-utils/3.0.0-foss-2021b-MSc
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.
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Last modified on 29th March 2023