sequenza-utils 3.0.0-foss-2021b

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

To load the module for sequenza-utils 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-utils/3.0.0-foss-2021b

BEAR Apps Version

2021b

Architectures

EL8-cascadelakeEL8-haswellEL8-icelakeUbuntu20.04-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.

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

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-2020a-Python-3.8.2-R-4.0.0 2020a

Last modified on 10th August 2022