GRIAL

GRIAL (Geometric Rules Inversion ALgorithm) is a software for predicting inversions and refining their breakpoints based on the computation of some geometric rules specific to inversions in a paired-end mapping (PEM) assay. GRIAL can also score the predicted inversions based on the number of concordant PEMs in the region of the inversion, and the expected number of discordant PEMs supporting each breakpoint given the inversion size, the repetitive nature of the sequence of the breakpoints, and the sequencing coverage.

Features
The features included in the algorithm are the following:

  • Preprocessig step: Given a set of discordant PEMs for inversions, GRIAL preprocesses the data to remove duplicated PEMs, PEMs with overlapping ends, or PEMs mapping to repeats.
  • Histogram clustering: GRIAL implements this clustering method to determine clusters of PEMs supporting the same inversion breakpoint.
  • Inversion definition and Breakpoint narrowing: GRIAL defines predictions of inversions based on one or two clusters of PEMs supporting one or the two inversion breakpoints, respectively, and narrow the breakpoints location based on these clusters.
  • Scoring: GRIAL scores the predicted inversions based on the number of concordant PEMs in the region of the inversion, and the expected number of discordant PEMs supporting each breakpoint given the inversion size, the repetitive nature of the sequence of the breakpoints, and sequencing coverage.

Versions
The first public version of GRIAL (April 2014) is GRIAL v.3.2.

Citing
If you use GRIAL in your research, please cite: Martínez-Fundichely et al. (in preparation).

Download GRIAL
The GRIAL code is available for download in a GitHub public repository at http://github.com/caceres-lab/GRIAL-code/archive/master.zip, including a complete user’s manual. GRIAL sample data is also available at http://github.com/caceres-lab/GRIAL-sampledata/archive/master.zip.

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