Tag: Structural Variations

Ulysses 1.0 – Accurate Detection of Low-frequency Structural Variations in large Insert-size Sequencing libraries

Ulysses 1.0

:: DESCRIPTION

Ulysses is a chimeric python/R tool that is designed to provide an accurate detection of low-frequency structural variations in large insert-size sequencing libraries

::DEVELOPER

Laboratory of Computational and Quantitative Biology (LCQB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R/ Python

:: DOWNLOAD

 Ulysses

:: MORE INFORMATION

Citation

Ulysses: Accurate detection of low-frequency structural variations in large insert-size sequencing libraries.
Gillet-Markowska A, Richard H, Fischer G, Lafontaine I.
Bioinformatics. 2014 Nov 7. pii: btu730.

RSVSim 1.24.0 – an R/Bioconductor package for the Simulation of Structural Variations

RSVSim 1.24.0

:: DESCRIPTION

RSVSim is a package for the simulation of deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.

::DEVELOPER

 Christoph Bartenhagen <christoph.bartenhagen at uni-muenster.de>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/ MacOsX
  • R
  • BioCOnductor

:: DOWNLOAD

 RSVSim

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):1679-81. doi: 10.1093/bioinformatics/btt198. Epub 2013 Apr 25.
RSVSim: an R/Bioconductor package for the simulation of structural variations.
Bartenhagen C, Dugas M.

Breakway 0.7.1 – Identify Structural Variations in Genomic Data

Breakway 0.7.1

:: DESCRIPTION

Breakway is a suite of programs that take aligned genomic data and report structural variation breakpoints.

::DEVELOPER

Michael James Clark

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • Perl

:: DOWNLOAD

 Breakway

:: MORE INFORMATION

Citation

Clark MJ, Homer N, O’Connor BD, Chen Z, Eskin A, et al. (2010)
U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line.
PLoS Genet 6(1): e1000832. doi:10.1371/journal.pgen.1000832