Event Detection

Detects events from raw signal in nanopore fast5 files

Installation:

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

Usage

./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.