ont-remora 2.0.0-foss-2022a

Methylation/modified base calling separated from basecalling. Remora primarily provides an API to call modified bases for basecaller programs such as Bonito. Remora also provides the tools to prepare datasets, train modified base models and run simple inference.

Accessing ont-remora 2.0.0-foss-2022a

To load the module for ont-remora 2.0.0-foss-2022a please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load bear-apps/2022a
module load ont-remora/2.0.0-foss-2022a

There is a GPU enabled version of this module: ont-remora 2.0.0-foss-2022a-CUDA-11.7.0

BEAR Apps Version

2022a

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.

Extensions

  • iso8601 1.1.0
  • lib_pod5 0.1.5
  • ont-remora-2.0.0
  • pod5 0.1.5
  • thop 0.1.1.2209072238
  • vbz_h5py_plugin 1.0.1

More Information

For more information visit the ont-remora website.

Dependencies

This version of ont-remora has a direct dependency on: Arrow/8.0.0-foss-2022a foss/2022a h5py/3.7.0-foss-2022a Pysam/0.20.0-GCC-11.3.0 Python/3.10.4-GCCcore-11.3.0 python-parasail/1.3.3-foss-2022a PyTorch/1.12.1-foss-2022a scikit-learn/1.1.2-foss-2022a SciPy-bundle/2022.05-foss-2022a tqdm/4.64.0-GCCcore-11.3.0

Other Versions

These versions of ont-remora 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
2.0.0-foss-2022a-CUDA-11.7.0 2022a

Last modified on 23rd January 2023