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[last edited on July, 7, 2015]


TakeABreak is a tool that can detect inversion breakpoints directly from raw NGS reads, without the need of any reference genome and without de novo assembling the genomes. Its implementation has a very limited memory impact allowing its usage on common desktop computers and acceptable runtime (Illumina reads simulated at 2x40x coverage from human chromosome 22 can be treated in less than two hours, with less than 1GB of memory).

Short presentation

Here are a few slides about TakeABreak: Lemaitre_alcob2014.pdf


Claire Lemaitre, Liviu Ciortuz and Pierre Peterlongo. 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. (Springer link)


Licensing A-GPL: Please read and agree this license before downloading.



  • TakeABreak-1.1.2 [July, 7, 2015], new options to deal with mutliple datasets in input and abundance-min threshold can now be automatically inferred from the data.
  • TakeABreak-1.1.1 [February, 12, 2015], new options to select solid kmers when mutliple datasets in input (now built on official release of gatb-core version 1.0.6).
  • TakeABreak-1.1.0 [December, 4, 2014], code reorganization: the script has been removed, it now comes as a single executable which makes it simpler to use. It is also faster thanks to improvements in the GATB library (kmer counting and graph building, gatb-core version 1.0.6beta).
  • TakeABreak-1.0.8 [September, 25, 2014], optimization of the main algorithm, amazing speed-up for large and complex genomes (from >4 days to <2 hours ! on a 300 Gbp mouse dataset)
  • TakeABreak-1.0.7 [September, 12, 2014], improved option management in script (required for integration in Galaxy)
  • TakeABreak-1.0.6 [June, 20, 2014], parallel version
  • TakeABreak_1.0.2 [March, 06, 2014], improved compatibility with older versions of gcc and/or clang
  • TakeABreak_1.0.1 [February, 13, 2014], New initial release 🙂 (source file distribution)
  • TakeABreak_1.0.0 [February, 06, 2014]. Initial release. Binary version.


Any comments or suggestions are warmly welcome. Don’t hesitate to send an email to claire-dot-lemaitre-at-inria-dot-fr