Genome Wide Analysis Tools One of the main causes of the fall of the Roman Empire was that, lacking zero, they had no way to indicate successful termination of their C Programs. (Robert Firth)

This is project homepage for the Genome Wide Analysis Tools project ("gwatools").

This collection of tools written in C++ with the STL library provides the basic building blocks to develop complex analysis pipelines on genomic coordinates.


TrackTool is a program designed to perform operations on genomic features in BED and BedGraph format.
It provides the basic building blocks to develop complex analysis pipelines on genomic coordinates.
TrackTool is around 60 times faster than other analysis tools for simple operations (intersections) on large input files, as those generated by Ultra-Deep sequencing experiments.
With TrackTool it is possible to perform sequences of operations (complex operations) on the input file without generating intermediate files. TrackTool is 50 times faster than existing tools for complex sequences of operations as for example:

"filter only features on the minus strand, expand those features 100 bases upstream and 50 bases downstream, calculate the overlap with known genes, for 1000 times shuffle the coordinates of known genes, calculate the overlap with this ensemble of random features".

The TrackTool's speed relies on a data structure with fast access (binary tree) and on the capability of performing several operations on the same data structure without generates intermediate files.





Download Genome Wide Analysis Tools files. Source code for this project is available as downloads or through the SVN repository used by the project, as accessible from the project develop page.


The the best way to get help with its software is by creating a new item in the Bugs Tracker.
For the documentation we have a wiki and you can ask question in the Help Forum


Contact Us

To contribute to this project, please contact the project administrators of this project, as shown on the project summary page.