A suite of tools for working with genome architecture mapping (GAM) datasets.


Genome architecture mapping (GAM) is a method for mapping the spatial proximity between genomic regions in the 3D nucleus. GAM works by cutting thin slices through nuclei, sequencing the DNA content and calculating the number of times different genomic regions appear together in the same slice.

GAMtools is a collection of utilities for working with GAM datsets. GAMtools can help you map raw sequencing files, analyze their genome coverage, perform quality control of GAM datasets and create proximity matrices.


The best place to get started with GAM is with the tutorial. You can find the GAMtools tutorial on our documentation website.

To work through the tutorial, you will need to download some example data, and you can also (optionally) download a custom Bowtie index (this makes the tutorial run a lot faster).


Beagrie RA, Scialdone A, Schueler M, Kraemer DC, Chotalia M, Xie SQ, Barbieri M, de Santiago I, Lavitas LM, Branco MR, Fraser J, Dostie J, Game L, Dillon N, Edwards PAW, Nicodemi M & Pombo, A.
Complex multi-enhancer contacts captured by Genome Architecture Mapping.
Nature (2017).

Download GAMtools

GAMtools is available on GitHub:

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Alternatively, you can install GAMtools from PyPi:

Download from PyPi

Or you can install GAMtools using pip:

$ pip install gamtools