ont_dap is a collection of bash scripts that (a) help install/ config tools commonly used to analyze Oxford Nanopore Technologies (ONT) sequencing data; and (b) streamline the use of these tools for sequencing performance and alignment analysis.

DISCLAIMER: the automated setup functionality is unfinished.

Dependencies

Mac or Linux OS
R >= 3.0.0
ggplot2
Python >= 2.7, < 3.0
pip
samtools

References for installing these:

pip: 	https://pip.pypa.io/en/latest/installing.html
R: 		https://www.r-project.org/
Python:	https://www.python.org/downloads/

The dependencies that will automatically be installed (if they are not already):

h5py >= 2.0.0
rpy2 >= 2.4.2
watchdog >= 0.8.3

Install/ Setup

WARNING: this is not fully functional; though it is still useful for seeing which packages need be installed.

$ git clone https://www.github.com/tmfarrell/ont_dap.git
$ cd ont_dap
$ source setup.sh

Usage

(1) Run poretools to assess sequencing run performance (Note: this should work provided all the dependencies for poretools installed properly):

$ ./run_poretools.sh -h

(2) Align and compute alignment statistics (Note: this works if samtools is installed):

$ ./run_alignment.sh -h

Contact: Tim Farrell, tfarrell01@gmail.com