sequenza-utils 3.0.0-foss-2022b

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-2022b

To load the module for sequenza-utils 3.0.0-foss-2022b please use this command on the BEAR systems (BlueBEAR, BEAR Cloud VMs, and CaStLeS VMs):

module load bear-apps/2022b
module load sequenza-utils/3.0.0-foss-2022b

BEAR Apps Version

2022b

Architectures

EL8-cascadelakeEL8-haswellEL8-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 Cloud and CaStLeS 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/2022b HTSlib/1.17-GCC-12.2.0 Python/3.10.8-GCCcore-12.2.0 R/4.3.1-foss-2022b SAMtools/1.17-GCC-12.2.0 sequenza/3.0.0-foss-2022b

Required By

This version of sequenza-utils is a direct dependent of: BEAR-Python-MSc-Bioinformatics/2022b-foss-2022b

Other Versions

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

Last modified on 9th August 2023