Flip-flop basecaller for Oxford Nanopore reads


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.

Available Versions

These versions of flappie are available on the BEAR systems (BlueBEAR and BEAR Cloud VMs). These will be retained in accordance with our Applications Support and Retention Policy.