Tag: Structural Variant

Fastbreak – Structural Variant Detection in Genomic data

Fastbreak

:: DESCRIPTION

Fastbreak is a set of python scripts implementing an O(n) algorithm for detecting translocations and other genetic structural variants from aligned mate pair sequence data in SAM/BAM format.

::DEVELOPER

Shmulevich Group

:: SCREENSHOTS

Fastbreak

:: REQUIREMENTS

  • Web Server
  • Tomcat
  • Java

:: DOWNLOAD

 Fastbreak

:: MORE INFORMATION

Citation

EURASIP J Bioinform Syst Biol. 2012 Oct 9;2012(1):15. doi: 10.1186/1687-4153-2012-15.
Fastbreak: a tool for analysis and visualization of structural variations in genomic data.
Bressler R, Lin J, Eakin A, Robinson T, Kreisberg R, Rovira H, Knijnenburg T, Boyle J, Shmulevich I.

BreakPtr 1.0.5 – Discovery of unbalanced Structural Variants with Tiling Microarrays

BreakPtr 1.0.5

:: DESCRIPTION

BreakPtr (abbrev. for Break-Pointer) is a computational approach for segmenting CGH data and analyzing chromosomal DNA sequence. Its Finder predicts breakpoints of large deletions and amplifications. Its Annotator identifies actual dosage ratios.

::DEVELOPER

Korbel Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 BreakPtr

:: MORE INFORMATION

Citation

Korbel JO, Urban AE, Grubert F, Du J, Royce TE, Starr P, Zhong, G, Emanuel BS, Weissman SM, Snyder M & Gerstein MB (2007)
Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome,
PNAS June 12, 2007 vol. 104 no. 24 10110-10115