BEAR Applications

flappie 2.0.0-foss-2019a-Python-3.7.2

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

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

2018b

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