= IGoR (_Inference and Generation Of Repertoires_) Documentation
Quentin Marcou
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IGoR is a C++ software designed to infer V(D)J recombination related
processes from sequencing data such as:

* Recombination model probability distribution
* Hypermutation model
* Best candidates recombination scenarios
* Generation probabilities of sequences (even hypermutated)

The following article describes the methodology, performance tests and
some new biological results obtained with IGoR:

https://www.nature.com/articles/s41467-018-02832-w[_High-throughput
immune repertoire analysis with IGoR_], _Nature Communications_, (2018)
Quentin Marcou, Thierry Mora, Aleksandra M. Walczak

Its heavily object oriented and modular style was designed to ensure
long term support and evolvability for new tasks in assessing TCR and
BCR receptors features using modern parallel architectures.

IGoR is a free (as in freedom) software released under the
https://www.gnu.org/licenses/quick-guide-gplv3.html[GNU-GPLv3] license.

[[version]]
Version
-------

include::./version.adoc[]


include::./general/installation.adoc[]

include::./general/workflow.adoc[]

include::./general/runtimes.adoc[]

include::./general/general_commands.adoc[]

[[working-directory]]
Working directory
^^^^^^^^^^^^^^^^^

This is where all IGoR outputs will appear. Specific folders will be
created for alignments, inference, evaluation and outputs.

include::./alignments/alignments.adoc[]

include::./inference/inference.adoc[]

include::./outputs/outputs.adoc[]

include::./generation/generation.adoc[]

include::./commands_examples/general.adoc[]

include::./general/advanced_usage.adoc[]

include::./general/cpp_interface.adoc[]

include::./general/python_interface.adoc[]

include::./general/contribute.adoc[]


[[contact]]
Contact
-------

For any question or issue please open an
https://github.com/qmarcou/IGoR/issues[issue] or email mailto:quentin.marcou@lpt.ens.fr[us].


Copying
-------
Free use of IGoR is granted under the terms of the https://www.gnu.org/licenses/quick-guide-gplv3.html[GNU General Public License version 3]
(GPLv3).
