.. _oa:

The ORGanelle ASseMbler principles
==================================

Sequencing strategies and file formats
--------------------------------------

Low-coverage shotgun sequencing of genomic DNA
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

The resulting data of low-coverage shotgun sequencing of genomic DNA (gDNA), aka genome skimming, is the primary data used by ``ORG.asm``. If we hypophethize that the organelle genomes represent several percent of the total gDNA, even with a modest depth of sequencing of the nuclear genome (around 1x coverage), on can hope to get more than 100x coverage for the organelle genomes and repeated regions (such as rDNA clusters). This allows the reconstruction of organelle genomes and repeated regions for up to 48 samples loaded in the same HiSeq 2500 lane. 

Raw sequencing results (after adapter trimming) are usually provided in the fastq format, the raw result of the assembly in fasta format and the annotated result (with CDS, tRNA, ...) in the EMBL format.


The file formats
^^^^^^^^^^^^^^^^

.. toctree::
   :maxdepth: 2

   fasta
   fastq
   embl


The ORGanelle ASseMbler commands
--------------------------------

Once installed, |Orgasm| enrich the command shell with the :ref:`oa <oa>` command. It is providing
a set of sub-commands allowing for the complete assembling of small genomes
(organelle genomes) from a genome skimming sequence dataset. You can have a
basic idea on how to proced by following the :doc:`tutorial <./mitochondrion>`.


.. figure:: command-flowgram.*
  :align: center
  :figwidth: 80 %
  :width: 500

  The :ref:`organelle assembler <oa>`'s provides a set of commands.

Several of these commands (at least three) have to executed to complete
an assembling process.

 - The bold green path indicates the minimal succession of
   commands you need to run to assemble a sequence from a set of illumina reads.
 - The green dotted path indicates an alternative succession of commands
   commonly run to achieve the assembling process.
 - The fine blue dotted arrows indicate the data used by each of the commands.
 - The fine red dotted arrows indicate the final results provided by commands.
 - The orange boxed commands correspond to utility commands not required for the
   assembling but sometime useful to get or restore some information.


The set of sub-commands can be splitted in several categories corresponding to
the main steps of the assembling procedure.

.. toctree::
   :maxdepth: 2

   preparing
   assembling
   finishing
   unfolding
   utilities
