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GAMtools: Utilities for working with Genome Architecture Mapping data.

GAMtools is a collection of utilities for working with Genome Architecture Mapping data. GAM is a technique for mapping 3D genome architecture by sequencing genomic DNA from thin nuclear sections (nuclear profiles or NPs). GAMtools can be used to automate the mapping and processing of sequencing data from NPs, to identify genomic regions present in each NP, and to calculate proximity matrices based on the co-segregation of genomic regions in a dataset of many NPs.

Tutorial

The GAMtools tutorial covers some of the basic use cases for GAMtools, and will guide you through re-mapping and re-processing of some example GAM data.

.. toctree::
   :maxdepth: 2
   :caption: Contents

   content/overview
   content/installation
   content/tutorial
   API documentation <api_docs/index>

.. toctree::
   :maxdepth: 2
   :glob:
   :caption: Tools

   tools/*

.. toctree::
   :maxdepth: 2
   :caption: GAMtools links

   Source code on GitHub <https://github.com/pombo-lab/GAMtools>
   Issue tracker <https://github.com/pombo-lab/GAMtools/issues>
   GAMtools paper <http://gam.tools/paper>
   Pombo lab website <https://pombolab.wordpress.com>


Indices and tables

License

GAMtools is freely available under the Apache License, Version 2.0