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Breakway 0.7.1 has been released!

Breakway: Identify Structural Variations in Genomic Data

Welcome to Breakway!

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

  • Takes in BAM formatted input, the current standard for genomic alignments.
    • Compatible with standard output from major alignment algorithms such as BFAST, BWA, MAQ, et cetera.
  • Capable of analyzing data from any major platform--Solexa, SOLiD, 454, et cetera.
  • Empirically identifies structural variation breakpoints.
  • Highly specific analysis generates very few false positives.
  • Includes a suite of downstream tools for annotating identified breakpoints and reducing false positives.

Breakway: The way to find structural variation breakpoints in your genome!


Get Breakway

Get Breakway by downloading from http://sourceforge.net/projects/breakway/files/.

Get Help

Forum Post

There is a thread at the SEQanswers forum that you can ask questions in.

Mailing Lists

Join the Breakway mailing lists!

  1. breakway-announce@lists.sourceforge.net
    Keep up to date on the latest updates to Breakway.
    [Click here to subscribe.]
  1. breakway-help@lists.sourceforge.net
    Get help using Breakway from the developers and other users.
    [Click here to subscribe.]
  1. breakway-devel@lists.sourceforge.net
    Interested in helping to develop Breakway? This is your connection.
    [Click here to subscribe.]

Breakway Compendium

The Breakway manual is stored interactively on this wiki: The Breakway Compendium

You can also find a PDF copy of the Compendium in the /manual/ folder of the Breakway download.


Breakway 0.7.1

A bug making Breakway incompatible with newer versions of Samtools has been fixed. Please update to the latest version!

Breakway 0.7

A new version of breakway.parameters.pl has been included in this updated package. It no longer depends on the dbampairedenddist from DNAA at all and simply takes in the parameters and BAM file previously used with dbampairedenddist to perform its function. Try it out! (See The Breakway Compendium for usage.)

Also, a bug involving the default score value (0) has been fixed.

Breakway 0.6

Breakway 0.6 includes a new script called "breakway.bwfilter.pl" as part of the Filtering Suite that allows one to cross-reference between the file being processed and another Breakway file. This is useful for projects such as comparing between a tumor and normal samples.

Citing Breakway

When using Breakway for your own work and publications, please cite this website "http://breakway.sourceforge.net" as well as the following paper:

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

About the Author

Michael James Clark is a senior graduate student in the Human Genetics Department at UCLA and a member of the Stan Nelson lab. He is a primary author of U87MG Decoded and wrote the first incarnation of Breakway as part of that project. In addition to Breakway, M.J. is involved in other whole genome sequencing studies. M.J. is also a regular contributor at the SEQanswers forum and posts there as Michael.James.Clark.

You may contact M.J. Clark with any questions or comments about structural variation analysis, or general genome sequencing and analysis. Please utilize the mailing lists for general questions about Breakway specifically. Media:Example.ogg

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