BEAR Applications

OptiType 1.3.2-foss-2018b-Python-3.6.6

OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles.

Accessing OptiType 1.3.2-foss-2018b-Python-3.6.6

To load the module for OptiType 1.3.2-foss-2018b-Python-3.6.6 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load OptiType/1.3.2-foss-2018b-Python-3.6.6

BEAR Apps Version

2020b

More Information

For more information visit the OptiType website.

Dependencies

This version of OptiType has a direct dependency on: foss/2018b future/0.16.0-foss-2018b-Python-3.6.6 GLPK/4.65-GCCcore-7.3.0 HDF5/1.10.2-foss-2018b matplotlib/3.0.0-foss-2018b-Python-3.6.6 Pyomo/5.5.0-foss-2018b-Python-3.6.6 Pysam/0.15.1-foss-2018b-Python-3.6.6 PyTables/3.4.4-foss-2018b-Python-3.6.6 Python/3.6.6-foss-2018b SAMtools/1.9-foss-2018b SeqAn/2.4.0-foss-2018b

Other Versions

These versions of OptiType 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.

Last modified on 5th June 2019