sequenza-utils 3.0.0-foss-2021b-MSc
Sequenza-utils is The supporting python library for the sequenza R package. Sequenza is a software for the estimation and quantification of purity/ploidy and copy number alteration in sequencing experiments of tumor samples. Sequenza-utils provide command lines programs to transform common NGS file format - such as BAM, pileup and VCF - to input files for the R package.Accessing sequenza-utils 3.0.0-foss-2021b-MSc
To load the module for sequenza-utils 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-utils/3.0.0-foss-2021b-MSc
BEAR Apps Version
Architectures
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.
More Information
For more information visit the sequenza-utils website.
Dependencies
This version of sequenza-utils has a direct dependency on: foss/2021b HTSlib/1.14-GCC-11.2.0 Python/3.9.6-GCCcore-11.2.0 R/4.2.0-foss-2021b SAMtools/1.15.1-GCC-11.2.0 sequenza/3.0.0-foss-2021b-MSc
Required By
This version of sequenza-utils is a direct dependent of: BEAR-Python-MSc-Bioinformatics/2021b-foss-2021b
Other Versions
These versions of sequenza-utils 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 |
---|---|
3.0.0-foss-2021b | 2021b |
3.0.0-foss-2020a-Python-3.8.2-R-4.0.0 | 2020a |
Last modified on 29th March 2023