==========================================================================================
**poretools**: *a toolkit for working with nanopore sequencing data from Oxford Nanopore.*
==========================================================================================
The MinION (TM) from Oxford Nanopore Technologies (ONT) is the first nanopore sequencer to be 
commercialised and is now available to early-access users. The MinION (TM) is a USB-connected, 
portable nanopore sequencer which permits real-time analysis of streaming event data. 
Currently, the research community lacks a standardized toolkit for the analysis of nanopore datasets.

We have therefore develped ``poretools``, a flexible toolkit for exploring datasets generated by 
nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. 
``Poretools`` operates directly on the native FAST5 (a variant of the HDF5 standard) file format produced 
by ONT and provides a wealth of format conversion utilities and data exploration and visualization tools. 

A preprint of the ``poretools`` manuscript is available on bioarxiv: http://biorxiv.org/content/early/2014/07/23/007401

Below are a few examples of common usage.

1. Extract sequences in FASTQ format from a set of FAST5 files.
    
.. code-block:: bash

    poretools fastq fast5/

2. Make a collector's curve of the yield from a sequencing run.

.. code-block:: bash

    poretools yield_plot --plot-type reads fast5/

3. Plot a histogram of read sizes from a set of FAST5 files.

.. code-block:: bash

    poretools hist fast5/

=================
Table of contents
=================

.. toctree::
   :maxdepth: 3

   content/installation
   content/help
   content/notebook
   content/examples

=================
Requirements
=================
  - HDF5 >= 1.8.7 (http://www.hdfgroup.org/HDF5/)
  - R >= 3.0.0
  - Python >= 2.7
  - rpy2 >= 2.4.2
  - h5py >= 2.0.0

.. note::
    Please note that Anaconda and Python(x,y) already have all these dependencies installed, other than R/Rpy2:
    Anaconda (Linux, Windows, OS X): https://store.continuum.io/cshop/anaconda/ Python(x,y) (Windows): https://code.google.com/p/pythonxy/


