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.


  • 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

  • Supports assembly files from ABySS 1.3.4
  • Supports reading FASTA index (*.fai) for generating NXX-plots and assembly statistics
  • 3 assembly types for the Navigator view: unitigs (aka single-end assembly), contigs (aka paired-end assembly), scaffolds
  • Fixes a bug where loading graph files takes a long time

Java web start link
For all platforms

JAR file and external libraries
For all platforms (6.4 MB)

Sample k32 E.coli assembly from ABySS 1.3.4
For all platforms (5.4 MB)

All Releases

Version Released Description Licenses Status
1.3.4 Jul 20, 2012 Version 1.3.4 supports assembly files from ABySS 1.3.4. 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. BCCA (academic use) final
1.0.1 Jun 01, 2010 Fixed bug causing errors when loading some ABySS graphs. BCCA (academic use) final
1.0 Feb 26, 2010 Initial ABySS-Explorer release. AFL final
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