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#Welcome to the VizBin wiki!
You can find information on the usage of VizBin but also on setting up a minimal build environment.
Should VizBin notify you about too little available memory and restart, this is usually related to the fact that the Java VirtualMachine has too little heap memory available. In this case, you have to let Java know that it can reserve more heap memory by running:
java -jar -Xmx3g VizBin-dist.jar
in the console, where -Xmx3g informs Java that it should reserve 3GB of memory. This works for Linux and Mac OS X and instructions for Windows will soon follow.
There are several reasons possible for why this can occur. It might be that you have a large amount of sequences and/or very long sequences. While the latter is a less frequent problem, a large amount of sequences is usually the reason why an Out-of-memory error occurs.
Alternatively, through clicking on Show additional options, setting a smaller k-mer size (i.e., Kmer length: 4) is possible. However, this is only suggested when your dataset is relatively large, i.e., contains around or above 50,000 - 100,000 sequences. This may be used in combination with the -Xmx option above for very large datasets.
Documentation on how to save/load embeddings is provided here.
Creating an image of the actual visualization is also easy with VizBin. A tutorial is given in the screenshot documentation.
