Commit 50ec92a3 by Frédéric Boyer

Reformat Toc and oa section

parent 8571799f
......@@ -12,7 +12,6 @@ Contents:
:maxdepth: 2
install
strategies
oa
mitochondrion
algorithms
......
.. _oa:
The ORGanelle ASseMbler command line
====================================
The ORGanelle ASseMbler principles
==================================
|Orgasm| is run using the :ref:`oa <oa>` Unix command. It is providing
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>`.
The ORGanelle ASseMbler commands
--------------------------------
.. figure:: command-flowgram.*
:align: center
......
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 (see 3. structure of an entry, of the ENA user manual ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/usrman.txt).
The file formats
----------------
.. toctree::
:maxdepth: 2
fasta
fastq
embl
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