Detects events from raw signal in nanopore fast5 files
HDF5 must be installed. Libraries and headers should be in system paths (ie $LD_LIBRARY_PATH and $CPATH respectively), or specified by running python setup.py build_ext --library-dirs <hdf5-location>/lib --include-dirs <hdf5-location>/include prior to installation.
git clone --recursive https://github.com/skovaka/event_detection.git
cd event_detection
make
./detect_events <fast5-path>
Outputs event tab separated mean, standard deviation, raw length, and raw start on each line.
Optional arguments:
--win-len1 = 3--win-len2 = 6--thresh1 = 1.4--thresh2 = 9.0--peak-height = 0.2--min-mean = 30(events with lower mean pA will not be output)--max-mean = 150(events with higher mean pA will not be output)--raw-start = 0(first sample to use for event detection)--raw-len = <FULL LENGTH>(number of samples to use for event detection)
I don't have a great understanding of the first four parameters, beyond that the average event length seems to be between win-len1 and win-len2. I will work on this.