BEAR Applications

transIndel 7098bd6-foss-2018b-Python-2.7.15-ScanNeo

Deprecated: Use of this version of transIndel is deprecated. More information on our Applications Support and Retention Policy.

transIndel is used to detect indels (insertions and deletions) from DNA-seq or RNA-seq data by parsing chimiric alignments from BWA-MEM.

Accessing transIndel 7098bd6-foss-2018b-Python-2.7.15-ScanNeo

To load the module for transIndel 7098bd6-foss-2018b-Python-2.7.15-ScanNeo please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load transIndel/7098bd6-foss-2018b-Python-2.7.15-ScanNeo

BEAR Apps Version

2018b

Architectures

EL8-cascadelake — EL8-haswell — Ubuntu20.04-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 transIndel website.

Dependencies

This version of transIndel has a direct dependency on: foss/2018b HTSeq/0.11.0-foss-2018b-Python-2.7.15 Pysam/0.15.1-foss-2018b-Python-2.7.15 Python/2.7.15-foss-2018b

Other Versions

These versions of transIndel 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 16th August 2019