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:
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MacOS-X 10.9 or above. (Intel 64bit processors) |
Download |
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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
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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.
