Commit d4224c06 by Frédéric Boyer

First version of the paragraph on the assembly graph

parent 108d62a1
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The assembly graph
------------------
|Orgasm| rely on a graph representation of the ongoing assembly. The graph used is what is
called a `De Bruijn graph <https://en.wikipedia.org/wiki/De_Bruijn_graph>`_ but restricted
to nodes representing substrings of a given length of the genome to reconstruct.
.. figure:: ./graph.*
:align: center
:figwidth: 80 %
:width: 500
An example of the underlying graph (adapted from `Compeau et al. (2011) <http://www.nature.com/nbt/journal/v29/n11/full/nbt.2023.html>`_)
In our particular case, we work with words of the length of the reads produced by the shotgun
sequencing. So the graph is also what is called a string graph for our set of reads (see
`Meyers (2005) <http://bioinformatics.oxfordjournals.org/content/21/suppl_2/ii79.abstract>`_
for details).
......@@ -5,6 +5,8 @@ The ORGanelle ASseMbler principles
.. include:: ./strategy.txt
.. include:: ./assembly-graph.txt
The ORGanelle ASseMbler commands
--------------------------------
......
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