BEAR Applications

flappie 2.0.0-foss-2019a-Python-3.7.2

Flip-flop basecaller for Oxford Nanopore reads

Accessing flappie 2.0.0-foss-2019a-Python-3.7.2

To load the module for flappie 2.0.0-foss-2019a-Python-3.7.2 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load flappie/2.0.0-foss-2019a-Python-3.7.2

BEAR Apps Version

2019a

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.

Runnie

Runnie is an experimental basecaller that works in 'run-length encoded' space. Basecalling using runnie is a two-stage process: firstly, a .run file is created containing the Run-Length Compressed (RLC) basecall, along information about the likely length of each run, then this is decoded into a fasta basecall. The executable runnie performs the initial RLC basecall, which is then processed by the python $EBROOTFLAPPIE/bin/decode_runnie.py script.

More Information

For more information visit the flappie website.

Dependencies

This version of flappie has a direct dependency on: foss/2019a HDF5/1.10.5-gompi-2019a Python/3.7.2-GCCcore-8.2.0 SciPy-bundle/2019.03-foss-2019a

Other Versions

These versions of flappie 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 12th November 2019