Commit 108d62a1 by Frédéric Boyer

Merge branch 'master' of git.metabarcoding.org:org-asm/org-asm

parents 4d023153 e918ff27
......@@ -57,6 +57,18 @@ Graph initialisation options
.. include:: ../options/seeds.txt
.. code-block:: bash
$ oa buildgraph --seeds 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
``--seeds`` options one for each class of sequences.
.. code-block:: bash
$ oa buildgraph --seeds protChloroArabidopsis --seeds rDNAChloro.fasta seqindex
.. _buildgraph.kup:
.. include:: ../options/kup.txt
......@@ -64,6 +76,17 @@ Graph initialisation options
Graph extension options
+++++++++++++++++++++++
The main aim of the :program:`buildgraph` command is to build the De Bruijn Graph which
is the central data structure used by the :ref:`organelle assembler <oa>`. This building is
done by two algorithms:
- the *extension* algorithm which is the main one
- the *fillgap* algorithm which is run when the first one failed to rescue the assembling procedure.
The *extension* algorithm is actually an heuristics and several parametters can be set to adapt the
efficiency of the algorithm to your data. Without precising them, these parameters are automatically
estimated from the dataset.
.. figure:: ../extension.*
:align: center
:figwidth: 80 %
......@@ -109,9 +132,17 @@ Graph extension options
Graph filtering options
+++++++++++++++++++++++
This set of options allows for excluding some reads from the assembling procedure.
.. option:: --lowcomplexity
Use also low complexity probes
Use also low complexity probes. Probes are the 3' end of
the sequence currently extended. By default probes with
a low complexity are not used during the graph extension
procedure. A probe is defined as a low complexity probe if
it is fully composed of an homopolymer or an homo-dimer or
an homo-trimer.
.. option:: --adapt5 adapt5
......@@ -132,7 +163,10 @@ Graph limit option
.. option:: --assmax BUILDGRAPH:ASSMAX
maximum base pair assembled
Maximum base pair assembled. This limit the size of the
De Bruijn Graph, and must be set to a larger value than
the size of the sequence you want to assemble to take into
account all the alternative paths present in the De Bruijn Graph.
Graph cleaning options
++++++++++++++++++++++
......
......@@ -51,6 +51,19 @@ Graph initialisation options
.. include:: ../options/seeds.txt
.. code-block:: bash
$ oa seeds --seeds 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
``--seeds`` options one for each class of sequences.
.. code-block:: bash
$ oa seeds --seeds protChloroArabidopsis --seeds rDNAChloro.fasta seqindex
.. _seeds.kup:
.. include:: ../options/kup.txt
.. option:: --back ORGASM:BACK
The number of bases taken at the end of contigs to
jump with pared-ends [default: <estimated>]
jump with paired-ends [default: <estimated>]
......@@ -10,16 +10,5 @@
- ``protMitoCapra``
- ``protMitoMachaon``
.. code-block:: bash
$ oa buildgraph --seeds 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
``--seeds`` options one for each class of sequences.
.. code-block:: bash
$ oa buildgraph --seeds protChloroArabidopsis --seeds rDNAChloro.fasta seqindex
\ No newline at end of file
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