Tag: Genomic Rearrangement

nFuse 0.2.1 – Discovery of Complex Genomic Rearrangements in Cancer

nFuse 0.2.1

:: DESCRIPTION

nFuse is a tool for detecting fusion transcripts and associated complex genomic rearrangements from matched RNA-seq and whole genome shotgun sequencing.nFuse predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS).

::DEVELOPER

Andrew McPherson (andrew.mcpherson@gmail.com)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 nFuse

:: MORE INFORMATION

Citation:

McPherson AW, Wu C, Wyatt A, Shah SP, Collins C, Sahinalp SC.
nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing.
Genome Res. 2012 Jun 28.

DCJ2HP – Bayesian Sampling of Genomic Rearrangement Scenarios via Double Cut and Join

DCJ2HP

:: DESCRIPTION

DCJ2HP is a software of Bayesian sampling of genomic rearrangement scenarios via double cut and join. The Double Cut and Join (DCJ) model, while less relevant, is computationally easier than the Hannenhalli–Pevzner (HP) model. The author use the computational facilities of the DCJ model to draw a sampling of HP scenarios. It is based on a parallel MCMC method that cools down DCJ scenarios to HP scenarios

::DEVELOPER

István Miklós ,   Eric Tannier

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsx
  • Java

 DCJ2HP

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Dec 15;26(24):3012-9. Epub 2010 Oct 29.
Bayesian sampling of genomic rearrangement scenarios via double cut and join.
Miklós I, Tannier E.

Cassis 1.0 – Detect Genomic Rearrangement Breakpoints

Cassis 1.0

:: DESCRIPTION

Cassis is a software for precise detection of rearrangement breakpoints in whole (sequenced and assembled) genomes.

::DEVELOPER

Cassis team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Cassis

:: MORE INFORMATION

Citation

Baudet, C., Lemaitre, C., Dias, Z., Tannier, E., Tannier, E., Gautier, C., and Sagot, M.-F. (2010).
Cassis : precise detection of genomic rearrangement breakpoints.
Bioinformatics, 26(15), 1897-1898.