DiscoPlot 1.0.0

DiscoPlot
=========

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:target: https://pypi.python.org/pypi/DiscoPlot/
:alt: Latest Version

.. image:: https://pypip.in/download/DiscoPlot/badge.svg
:target: https://pypi.python.org/pypi/DiscoPlot/
:alt: Downloads

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:target: https://travis-ci.org/BeatsonLab-MicrobialGenomics/DiscoPlot
:alt: Build status

DiscoPlot allows the user to quickly identify genomic rearrangements,
misassemblies and sequencing artefacts by providing a scalable method for
visualising large sections of the genome. It reads single-end or paired read
alignments in SAM, BAM or standard BLAST tab format and creates a scatter
plot of opaque crosses representing the alignments to a reference.
DiscoPlot is freely available (under a GPL license) for download (Mac OS
X, Unix and Windows) at:
https://github.com/BeatsonLab-MicrobialGenomics/DiscoPlot/releases.

.. image:: https://raw.githubusercontent.com/BeatsonLab-MicrobialGenomics/DiscoPlot/master/pictures/Figure_3_lowres.gif
:target: https://raw.githubusercontent.com/BeatsonLab-MicrobialGenomics/DiscoPlot/master/pictures/Figure_3.gif
:alt: DiscoPlot figure

**DiscoPlot of a mock genome.** A mock genome was created by adding genomic
rearrangements to the chromosome of E. coli str. UTI89. Paired-end reads
generated from the mock genome (query) with GemSim and mapped back to UTI89
(reference). The first ~500 Kbp were then visualised using DiscoPlot.


Documentation
-------------

Please use this README.rst as the core DiscoPlot user documentation.


Citation
--------

Cite this Github repository if you use DiscoPlot to generate figures
for publications::

SULLIVAN MJ & BEATSON SA^.
DiscoPlot - Visualising discordant reads.
https://github.com/BeatsonLab-MicrobialGenomics/DiscoPlot.


TODO
----

On the roadmap:
* Sam compatibility
* Print selected read names, alignments or sequences


Installation
------------

DiscoPlot is a commandline application. If you're not familiar with the
commandline we recommend you ask local IT support to help you install it.

You will need to install/have installed:
* python >= 2.7 (**Python 3 is not supported**)

To automatically generate BLAST aligments (For long read DiscoPlots) using
DiscoPlot you will need to install/have installed:
* ncbiblast+ >= 2.2.27

You can check these are installed by::

$ python --version
$ blastn -version

Installation of python or blastn (without a package manager) is beyond the
scope of this document.

If you have both python and blastn you need to (if not already present)
install pip_.

You can check if pip_ exists with::

$ which pip

If you get a "not found", please read the `pip installation instructions`_.

**If you already have pip we do suggest you upgrade it.** We are using version
1.5.6 at the time of writing this document.

You can upgrade pip_ like this::

$ pip install --upgrade pip


The following python libraries_ should be installed (automatically) if you follow
the installation instructions detailed below.

We use the following python libraries_:
* numpy >= 1.8.1
* matplotlib >= 1.3.1
* pysam >= 0.8.1

Pysam is only required for generating DiscoPlots with BAM files. SAM
compatability has been included to allow windows users to generate
DiscoPlots. PySam will not install on Windows, don't bother trying (or if
you've succeeded please let me know how).


Linux (Ubuntu)
~~~~~~~~~~~~~~

Discoplot uses 3rd party packages that are extremely important for scientific
computing but may be difficult to install. While *pip install *
*--user DiscoPlot* may work we recommend you install these 3rd party packages
using apt-get.

Run::

$ sudo apt-get install python-numpy python-matplotlib

Now pip_ install DiscoPlot::

$ pip install --user DiscoPlot

We use the --user option of pip_ to put DiscoPlot in: /home/$USER/.local/bin/
You need to add this location to you ~/.bash_profile.

Add DiscoPlot to your path::

$ echo 'export PATH=$PATH:/home/$USER/.local/bin/' >> ~/.bash_profile

Finally install BLAST+::

$ sudo apt-get install ncbi-blast+


MacOSX (Mavericks)
~~~~~~~~~~~~~~~~~~

**You'll need to have the equivalents of python-dev libatlas-dev liblapack-dev
gfortran libfreetype6-dev libfreetype6 & libpng-dev installed.** We had no
problems installing DiscoPlot on a recently acquired OSX Mavericks machine
using the homebrew package manager.

The installed packages on this machine via::

$ brew list

Are available at this gist_.

pip install DiscoPlot::

$ pip install --user DiscoPlot

We use the --user option of pip_ to put DiscoPlot in: /home/$USER/.local/bin/
You need to add this location to you ~/.bash_profile.

Add DiscoPlot to your path::

$ echo 'export PATH=$PATH:/home/$USER/.local/bin/' >> ~/.bash_profile

Finally install BLAST+::

$ sudo brew install blast


Testing DiscoPlot Installation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Run::

$ DiscoPlot -h
$ python -c 'import DiscoPlot; print DiscoPlot'





Upgrading DiscoPlot
~~~~~~~~~~~~~~~~~~~

You can upgrade like this::

pip install --upgrade DiscoPlot

**Please regularly check back to make sure you're running the most recent
DiscoPlot version.**


Example of figures produced by DiscoPlot
----------------------------------------

.. image:: https://raw.githubusercontent.com/BeatsonLab-MicrobialGenomics/DiscoPlot/master/pictures/Figure_3_lowres.gif
:target: https://raw.githubusercontent.com/BeatsonLab-MicrobialGenomics/DiscoPlot/master/pictures/Figure_3.gif
:alt: DiscoPlot figure
:align: center

**DiscoPlot of a mock genome.** A mock genome was created by adding genomic
rearrangements to the chromosome of E. coli str. UTI89. Paired-end reads
generated from the mock genome (query) with GemSim (ref) and mapped back to
UTI89 (reference). The first ~500 Kbp were then visualised using DiscoPlot.

.. image:: https://raw.githubusercontent.com/BeatsonLab-MicrobialGenomics/DiscoPlot/master/pictures/Figure_4_lowres.gif
:target: https://raw.githubusercontent.com/BeatsonLab-MicrobialGenomics/DiscoPlot/master/pictures/Figure_4.gif
:alt: DiscoPlots of structural variants
:align: center

**DiscoPlots of common structural variants.** Each box shows a common genomic
rearrangement represented by a DiscoPlot. Rows A and B were created using
100 bp long paired-end reads with an insert size of 300bp. Rows C and D were
created using single-end reads with an average length of 1000bp.
For each box the rearrangement in the sequenced genome is listed, followed by
the scale of the gridlines in brackets.
A1, C1: 300 bp deletion (400 bp). A2, C2: 300 bp insertion (400 bp).
A3, C3: 300 bp inversion (400 bp).
A4, C4: 300 bp sequence translocated 50 Kbp upstream (10 Kbp).
B1, D1: 3000 bp deletion (1000 bp).
B2, D2: 3000 bp insertion (500 bp). B3, D3: 3000 bp inversion (1000 bp).
B4, D4: 3000 bp sequence translocated 50 Kbp upstream (10 Kbp). C1)

.. image:: https://raw.githubusercontent.com/BeatsonLab-MicrobialGenomics/DiscoPlot/master/pictures/Figure_5_lowres.png
:target: https://raw.githubusercontent.com/BeatsonLab-MicrobialGenomics/DiscoPlot/master/pictures/Figure_5.png
:alt: DiscoPlot of E. coli genome
:align: center

**The dynamic nature of the genome of Escherichia coli str. UTI89.** Discoplot
of paired-end reads from a clonal culture of UTI89 mapped back to the
published reference chromosome and plasmid (top). A) Zoomed region of the
DiscoPlot, a small inversion exists in some of the sequenced bacteria. Four
of these sites, corresponding to known prophage regions, were identified
using DiscoPlot. B) Close up of the plasmid in the DiscoPlot. Each entry
in the alignment file is separated by an opaque green line. A large inversion
has been identified, this region corresponds to an inverted repeat found in the
plasmid. The cross in the lower right corner indicates that this region
circularises.


Tutorials
---------

**Coming Soon**


Commands
--------

To see a full list of flags type DiscoPlot --help

Detailed descriptions coming soon




.. _pip: http://www.pip-installer.org/en/latest/
.. _libraries: https://github.com/BeatsonLab-MicrobialGenomics/DiscoPlot/blob/master/requirements.txt
.. _gist: https://gist.github.com/mscook/ef7499fc9d2138f17c7f
.. _pip installation instructions: http://pip.readthedocs.org/en/latest/installing.html