ABySS-Explorer

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This product has not had a release in over 1 year and may no longer be maintained.

A sequence assembly visualization tool

Project Description

ABySS-Explorer is an interactive Java application that employs a novel graph-based representation to display a sequence assembly and associated meta data. The tool was designed with the ABySS sequence assembler in mind and was motivated by the need to examine assembly structure, in particular contig connectivity and supporting paired-end read relationships.

Publications:

  • ABySS-Explorer: Visualizing genome sequence assemblies. Nielsen CB, Jackman SD, Birol I, Jones SJM. IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization / Information Visualization 2009). 2009. 15(6):881-8. Best Paper Award (PubMed
  • De novo Transcriptome Assembly with ABySS. Birol İ, Jackman SD, Nielsen CB, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, Horsman DE, Connors JM, Gascoyne RD, Marra MA and Jones SJM. Bioinformatics. 2009. 1;25(21):2872-7. (PubMed)

Current Release
ABySS-Explorer 1.3.4

Released Jul 20, 2012

Version 1.3.4 supports assembly files from ABySS 1.3.4.
More about this release…

Download file Get ABySS-Explorer for all platforms
Java web start link
Download file Get ABySS-Explorer for all platforms
JAR file and external libraries
Download file Get ABySS-Explorer for all platforms
Sample k32 E.coli assembly from ABySS 1.3.4
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All Releases

Version Released Description Compatibility Licenses Status
1.3.4 Jul 20, 2012 Version 1.3.4 supports assembly files from ABySS 1.3.4. More about this release… BCCA (academic use) final
1.3.0 Nov 28, 2011 Version 1.3.0 is compatible with assemblies generated from ABySS 1.3.0 or above. In addition to visualizing ABySS assemblies as graphs, it also displays contiguity statistics and plots. More about this release… BCCA (academic use) final
1.0.1 Jun 01, 2010 Fixed bug causing errors when loading some ABySS graphs. More about this release… BCCA (academic use) final
1.0 Feb 26, 2010 Initial ABySS-Explorer release. More about this release… AFL final
Project Resources

Project owner: Cydney Nielsen