Jvarkit
Java utilities for Bioinformatics
Documentation is available at: [https://jvarkit.readthedocs.io/](https://jvarkit.readthedocs.io/) The project is written primarily in Java, distributed under the Other license, first published in 2013. Key topics include: bioinformatics, biology, genomics, java, next-generation-sequencing.
JVARKIT
Java utilities for Bioinformatics
Documentation
Documentation is available at: https://jvarkit.readthedocs.io/
Download
A pre-compiled jar is available at https://uncloud.univ-nantes.fr/index.php/s/4sL77oWR2BFzSBH .
Compilation
Since 2023, most tools (but not all) are now packaged into one application jvarkit.jar. Tools that were executed like java -jar toolname.jar are now executed as java -jar jvarkit.jar toolname. The documentation is not always up to date on this point.
See the documentation at https://jvarkit.readthedocs.io/.
Conda / Bioconda
A conda package created by DrYak is available at https://bioconda.github.io/recipes/jvarkit/README.html
Containers
jvarkit is available as a Singularity container under https://depot.galaxyproject.org/singularity/ .
GUI/Swing applications might not work.
Author
Pierre Lindenbaum PhD
Contributors
Showing top 11 contributors by commit count.
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