TakeABreak

TakeABreak detects inversion breakpoints without a reference genome by looking for fixed size topological patterns in the de Bruijn graph. TakeABreak requires small memory configuration and processes data quickly. For example,  Illumina reads simulated at 2x40x coverage from human chromosome 22 can be processed  in  2 hours and 1GB of memory.

Reference

C. Lemaitre, L. Ciortuz and P. Peterlongo. (2014) Mapping-free and assembly-free discovery of inversion breakpoints from raw NGS reads. Proceedings of AlCoB 2014, in Algorithms for Computational Biology, LNCS vol. 8542, pp. 119–130.

Ready-to-use executable

TakeABreak is available as a binary for immediate use on Linux and MacOSX platforms, with the following requirements:

maclogo MacOS-X 10.9 or above.
(Intel 64bit processors)
Download
linuxlogo Linux running on Intel or AMD 64bit processors.
(kernel 2.6.32 or above, GLIBCXX_3.4.13 or above)
Download

For all other platforms or configurations, or if above binaries fail to run on your computer, you should download source code and compile it.

Source Code

cpp-logo TakeABreak tool is fully written in C++. Download

Documentation

Available here.

License

TakeABreak binaries and source code are covered by the Affero GPL version 3 license.

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