Java utilities for Bioinformatics
Documentation is available at: https://jvarkit.readthedocs.io/
A pre-compiled jar is available at https://uncloud.univ-nantes.fr/index.php/s/4sL77oWR2BFzSBH .
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/.
A conda package created by DrYak is available at https://bioconda.github.io/recipes/jvarkit/README.html
jvarkit is available as a Singularity container under https://depot.galaxyproject.org/singularity/ . GUI/Swing applications might not work.
Pierre Lindenbaum PhD