ABySS-explorer

visual exploration of ABySS assembly data

Written by Ka Ming Nip

Copyright 2011 Canada's Michael Smith Genome Sciences Centre, BC Cancer

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Dependency 📌

• Java SE Runtime Environment (JRE) 8

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)

Libraries used:

• Apache Batik SVG Toolkit
• JFreeChart 1.0.18
• JUNG 2.0.1

These libraries are already included in the compiled package.

Installation 🔧

1. Download the binary tarball ABySS-explorer-X.X.X.tar.gz from the releases section.
2. Extract the downloaded tarball with the command:

tar -zxf ABySS-explorer-X.X.X.tar.gz

3. 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.

Java Options ☕

To limit the size of Java heap to 1GB:

java -Xmx1g -jar ABySS-explorer.jar ...

Other JVM options may also be used.

User Manual 📙

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.

Citation ✏️

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.

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