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.
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>
GAMtools is freely available under the Apache License, Version 2.0