Commit 5a6549d2 by Eric Coissac

Some updates into the documentation

parent 428af603
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doc/sphinx/source/command-flowgram.png

66.2 KB | W: | H:

doc/sphinx/source/command-flowgram.png

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doc/sphinx/source/command-flowgram.png
doc/sphinx/source/command-flowgram.png
doc/sphinx/source/command-flowgram.png
doc/sphinx/source/command-flowgram.png
  • 2-up
  • Swipe
  • Onion skin
......@@ -25,9 +25,14 @@ command prototype
.. code-block:: none
usage: oa buildgraph [-h]
[--seeds seeds] [--kup ORGASM:KUP]
[--reformat]
[--probes probes] [--kup ORGASM:KUP]
[--adapt5 adapt5] [--adapt3 adapt3]
[--phiX] [--phiX-off]
[--coverage BUILDGRAPH:COVERAGE]
[--coverage-ratio BUILDGRAPH:COVERAGE]
[--fillgaps-ratio BUILDGRAPH:COVERAGE]
[--lowcomplexity]
[--minread BUILDGRAPH:MINREAD]
[--minoverlap BUILDGRAPH:MINOVERLAP]
......@@ -35,6 +40,8 @@ command prototype
[--mincov BUILDGRAPH:MINCOV]
[--assmax BUILDGRAPH:ASSMAX]
[--smallbranches BUILDGRAPH:SMALLBRANCHES]
[--maxfillgaps]
[--clean] [--force-seeds] [--no-seeds seeds]
[--back ORGASM:BACK] [--snp]
index [output]
......@@ -50,16 +57,21 @@ General option
show the help message and exit
.. option:: --reformat
Asks for reformatting an old sequence assembly to the new
format
Graph initialisation options
++++++++++++++++++++++++++++
.. _buildgraph.seeds:
.. _buildgraph.probes:
.. include:: ../options/seeds.txt
.. code-block:: bash
$ oa buildgraph --seeds protChloroArabidopsis seqindex
$ oa buildgraph --probes protChloroArabidopsis seqindex
A set of seed sequences must be or nucleic or proteic. For initiating
assembling with both nucleic and proteic sequences you must use at least two
......
......@@ -115,14 +115,20 @@ command prototype
.. code-block:: none
usage: $ oa index [-h] [--single | --mate-pairs]
usage: $ oa index [-h] [--reformat]
[--single | --mate-pairs]
[--check-ids] [--check-pairing]
[--max-read ###]
[--max-read ###] [--skip ###]
[--check-phiX17|--no-check-phiX174]
[--length ### | --estimate-length #.##]
[--minimum-length ###]
[--5-prime-trim ###]
[--3-prime-quality ###] [--bad-quality ###]
[--fasta | --forward-fasta | --reverse-fasta]
[--no-pipe]
[--fastq-dump] [--bypass-filtering]
[--quality-encoding-offset]
[--no-pipe] [--low-memory]
<index> <forward_fastq_file> [reverse_fastq_file]
positional arguments
--------------------
......@@ -150,6 +156,12 @@ General option
show the help message and exit
.. option:: --reformat
Asks for reformatting an old sequence index to the new
format
Sequencing strategy
+++++++++++++++++++
......@@ -178,9 +190,49 @@ Sequence file checking
The two sequence with the ids `seqid/1` and `seqid/2` are
considered as paired.
Sequence quality checking
+++++++++++++++++++++++++
.. option:: --check-phiX174
Checks for PhiX174 contamination
.. option:: --no-check-phiX174
Does not check for PhiX174 contamination (default)
.. option:: --5-prime-trim ##
Cut the N first base pairs of reads (default 0bp)
.. option:: --3-prime-quality ##
Hard clips the 3' end of each readsafter the first
base with a score less or equal to Q (default 0 no
clipping)
.. option:: --bad-quality ##
Consider quality below Q as bad quality score, and try
to clip reads to maximise the overall quality. Zero
means no clipping (default 10)
.. option:: --skip ##
Skip the N first read pairs (default 0)
.. option:: --bypass-filtering
Sequence files are considered as pre-filtered fastq files
Limit for the indexation
++++++++++++++++++++++++
.. _index.max-read:
.. option:: --max-read ###
`###` indicates the number of millions of reads to index. If not
......@@ -227,9 +279,22 @@ Limit for the indexation
Indexes the `forward.fastq` and `reverse.fastq` files using a length
such as at least 90% of the reads will be indexed.
.. option:: --minimum-length ###
The minimum length of the read to index if the
*--estimate-length* option is activated (default 81)
.. option:: --fastq-dump
Dump the fastq file or the trimmed reads
Sequence file format
++++++++++++++++++++
.. _index.fasta:
.. option:: --fasta
Indicates than the two sequence files to index are :ref:`fasta <fasta>` files.
......@@ -238,6 +303,8 @@ Sequence file format
$ oa index --fasta seqindex forward.fasta reverse.fasta
.. _index.forward-fasta:
.. option:: --forward-fasta
Indicates than the forward file is a fasta file
......@@ -246,6 +313,8 @@ Sequence file format
$ oa index --forward-fasta seqindex forward.fasta reverse.fastq
.. _index.reverse-fasta:
.. option:: --reverse-fasta
Indicates than the reverse file is a fasta file
......@@ -254,6 +323,23 @@ Sequence file format
$ oa index --reverse-fasta seqindex forward.fastq reverse.fasta
.. _index.quality-encoding-offset:
.. option:: --quality-encoding-offset ##
The code offset added to each quality score to encode
fastq quality (default 33 - Sanger format)
.. code-block:: bash
$ oa index --quality-encoding-offset 64 seqindex forward.fastq reverse.fasta
Allows for reading old *Solexa* fastq format. Look at the FastQ format
Wikipedia web page to know what if the *quality encoding offset*
corresponding to your files.
If the file names end by `.gz` or `.bz2` they are considered as compressed
respectively by the `gzip`_ or the `bzip2`_ program and are uncompressed on the
fly. The :ref:`fasta <fasta>` related options can be combined without restriction with this
......@@ -271,11 +357,19 @@ compressed with `bzip2`_.
System option
+++++++++++++
.. _index.no-pipe:
.. option:: --no-pipe
By default the :ref:`organelle assembler <oa>` uses named pipes to transfer
data among programs. Using this option you can enforce to use
tempory files instead.
.. _index.low-memory:
.. option:: --low-memory
Reduce memory usage for optimal length computation
.. _`gzip`: http://www.gzip.org
.. _`bzip2`: http://www.bzip.org
......@@ -4,5 +4,5 @@ Finalizing the assembly
.. toctree::
:maxdepth: 2
commands/fillgaps
commands/buildgraph
commands/cutlow
......@@ -17,7 +17,7 @@ Prerequisites
To install the |orgasm|, you need that these softwares are installed on your
system:
* Python 3.4 (installed by default on most ``Unix`` systems, available from
* Python 3.5 (installed by default on most ``Unix`` systems, available from
`the Python website <http://www.python.org/>`_)
* ``gcc`` (installed by default on most ``Unix`` systems, available from the
GNU sites dedicated to `GCC <https://www.gnu.org/software/gcc/>`_ and
......@@ -32,9 +32,23 @@ On MacOSX
^^^^^^^^^
The C compiler and all the other compilation tools are included in the `XCode <https://itunes.apple.com/fr/app/xcode/id497799835?mt=12>`_
application not installed by default. Python3 is not prived by default. You have to install a complete distribution
application not installed by default. Python3 is not installed by default. You have to install a complete distribution
of Python that you can download as a `MacOSX package from the Python website <https://www.python.org/downloads/>`_.
Developer command line tools can also be installed using the following command line in a UNIX terminal
.. code-block:: bash
xcode-select --install
From the Mojaves version of MacOSX the C header have to be installed using the following commands
.. code-block:: bash
open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
Downloading and installing |orgasm|
...................................
......@@ -46,7 +60,7 @@ the |orgasm|. From a Unix terminal you must now run the command :
.. code-block:: bash
> python3 get-orgasm.py
python3 get-orgasm.py
The script will create a new directory at the place you are running it in which all the
|orgasm| will be installed. No system privilege are required, and you system will not
......@@ -61,13 +75,13 @@ by reconfiguring your Unix environment.
.. code-block:: bash
> ./orgasm
./orgasm
Once activated you can desactivate |orgasm| by typing the command ``exit``.
.. code-block:: bash
> exit
exit
ORG.asm are no more activated, Bye...
=====================================
......
......@@ -6,5 +6,3 @@ Unfolding the assembly graph
commands/unfold
commands/unfoldrdna
commands/path
commands/fasta
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