visual exploration of ABySS assembly data
Written by Ka Ming Nip
Copyright 2011 Canada's Michael Smith Genome Sciences Centre, BC Cancer
Check your Java version:
java -version
Example:
java version "1.8.0_101"
Java(TM) SE Runtime Environment (build 1.8.0_101-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.101-b13, mixed mode)
These libraries are already included in the compiled package.
- Download the binary tarball
ABySS-explorer-X.X.X.tar.gzfrom the releases section. - Extract the downloaded tarball with the command:
tar -zxf ABySS-explorer-X.X.X.tar.gz
- ABySS-explorer is ready to use, ie.
java -jar /path/to/ABySS-explorer.jar ...
There is nothing to compile/configure/build!
If you decide to move the files to another location, make sure ABySS-explorer.jar and lib/ are under the same directory.
To limit the size of Java heap to 1GB:
java -Xmx1g -jar ABySS-explorer.jar ...
Other JVM options may also be used.
Our user manual is available for download as a PDF file. The current version is almost identical to version 1.3.x. An updated user manual for the current version will be made available.
If you use ABySS-explorer for your research, please cite:
Nielsen CB, Jackman SD, Birol I, Jones SJ. ABySS-Explorer: visualizing genome sequence assemblies. IEEE Trans Vis Comput Graph. 2009 Nov-Dec;15(6):881-8. doi: 10.1109/TVCG.2009.116.