Commit 54173c1a by Eric Coissac

Documentation writing marathon

parent c128b846
......@@ -48,7 +48,7 @@ General option
.. option:: -h, --help
show the help message and exit
show the help message and exit
Graph initialisation options
++++++++++++++++++++++++++++
......@@ -77,9 +77,9 @@ Graph extension options
the minimum count of read to consider [default:
<estimated>]
.. code-block:: bash
$ oa buildgraph --seeds protChloroArabidopsis --minread 5 seqindex
.. code-block:: bash
$ oa buildgraph --seeds protChloroArabidopsis --minread 5 seqindex
Consider an extension if at least five reads are present in the extension
stack.
......@@ -137,25 +137,27 @@ Graph limit option
Graph cleaning options
++++++++++++++++++++++
.. _buildgraph.smallbranches:
.. option:: --smallbranches BUILDGRAPH:SMALLBRANCHES
After a cycle a extension, if you observe the assembling graph
you can observe a main path and many small aborted branches surrounding
this main path. They correspond to path initiated by a sequencing
error or a nuclear copy of a chloroplast region not enough covered by
the skimming sequencing to be successfuly extended.
the skimming sequencing to be successfully extended.
One of the cleaning step consist in deleting these small branches.
This option indicates up to which lenght branches have to be deleted.
By default this legth is automaticaly estimated from the graph.
.. code-block:: bash
This option indicates up to which length branches have to be deleted.
By default this length is automatically estimated from the graph.
.. code-block:: bash
$ oa buildgraph --seeds protChloroArabidopsis \
--smallbranches 15 seqindex
During the cleaning steps, all the branches with a legth
shorter or equal to 15 base pairs will be deleted
During the cleaning steps, all the branches with a length
shorter or equal to 15 base pairs will be deleted
.. option:: --snp
When the data set correspond to a pool of individuals, it is possible
......@@ -174,16 +176,15 @@ Graph cleaning options
$ oa buildgraph --seeds protChloroArabidopsis \
--snp seqindex
Run the assembling, ignoring the SNPs.
Run the assembling, ignoring the SNPs.
Gap filling option
Scaffolding option
++++++++++++++++++
.. option:: --back ORGASM:BACK
.. _buildgraph.back:
The number of bases taken at the end of contigs to
jump with pared-ends [default: <estimated>]
.. include:: ../options/back.txt
.. _`bwa`: http://sourceforge.net/projects/bio-bwa/
.. _`yed`: https://www.yworks.com/en/products/yfiles/yed/
......@@ -2,3 +2,39 @@
The :program:`compact` command
==============================
The :ref:`organelle assembler <oa>`'s :program:`compact`
rebuild the `gml` file containing the compacted version of the assembling graph
from a previously asssembled dataset.
command prototype
-----------------
.. program:: oa buildgraph
.. code-block:: none
usage: oa buildgraph [-h]
[--back ORGASM:BACK]
index [output]
.. include:: ../options/positional.txt
optional arguments
------------------
General option
++++++++++++++
.. option:: -h, --help
show the help message and exit
Scaffolding option
++++++++++++++++++
.. _buildgraph.back:
.. include:: ../options/back.txt
......@@ -2,3 +2,81 @@
The :program:`cutlow` command
=============================
The :ref:`organelle assembler <oa>`'s :program:`cutlow`
redoes the cleaning step allowing to clean-out all the branches of the assembling graph
not reaching the coverage specified by the `--coverage` option.
realizes the assembling of the reads by building the De Bruijn Graph which
is the central data structure used by the :ref:`organelle assembler <oa>`.
.. figure:: ../oa-cutlow.*
:align: center
:figwidth: 80 %
:width: 500
The :ref:`organelle assembler <oa>`'s :program:`cutlow` command
re-executes all the cleaning task in red.
command prototype
-----------------
.. program:: oa buildgraph
.. code-block:: none
usage: oa cutlow [-h]
[--coverage BUILDGRAPH:COVERAGE]
[--smallbranches BUILDGRAPH:SMALLBRANCHES]
[--back ORGASM:BACK] [--snp]
index [output]
.. include:: ../options/positional.txt
optional arguments
------------------
General option
++++++++++++++
.. option:: -h, --help
show the help message and exit
Graph cleaning options
++++++++++++++++++++++
.. option:: --coverage BUILDGRAPH:COVERAGE
during the cutlow execution all stems with a coverage below the specified coverage
will be deleted [default:<estimated>]
.. _buildgraph.smallbranches:
.. option:: --smallbranches BUILDGRAPH:SMALLBRANCHES
After a cycle a extension, if you observe the assembling graph
you can observe a main path and many small aborted branches surrounding
this main path. They correspond to path initiated by a sequencing
error or a nuclear copy of a chloroplast region not enough covered by
the skimming sequencing to be successfully extended.
One of the cleaning step consist in deleting these small branches.
This option indicates up to which length branches have to be deleted.
By default this length is automatically estimated from the graph.
.. code-block:: bash
$ oa cutlow --smallbranches 15 seqindex
During the cleaning steps, all the branches with a length
shorter or equal to 15 base pairs will be deleted
Scaffolding option
++++++++++++++++++
.. _buildgraph.back:
.. include:: ../options/back.txt
\ No newline at end of file
......@@ -3,8 +3,8 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Org.Asm: |Orgasm|
=================
|Orgasm|
========
Contents:
......
doc/sphinx/source/oa-unfold.png

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doc/sphinx/source/oa-unfold.png

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doc/sphinx/source/oa-unfold.png
doc/sphinx/source/oa-unfold.png
doc/sphinx/source/oa-unfold.png
doc/sphinx/source/oa-unfold.png
  • 2-up
  • Swipe
  • Onion skin
.. option:: --back ORGASM:BACK
The number of bases taken at the end of contigs to
jump with pared-ends [default: <estimated>]
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