Just Another System for Epityping using NGSs data

Jasen is a pipeline for performing antibiotic resistance prediction and epityping of whole genome sequenced infectious bacteria.

Get started

• Get an overivew of the pipeline and the different bacterial species it supports.

• Get started with installing Jasen.

• Analyze your first sample.

Report and visualisation

• Bonsai: Visualises jasen outputs.

• graptetree: Visualise phylogenetic relationship using cgmlst data.

Tips

• Always run the latest versions of the bioinformatical software.

• Verify you have execution permission for jasens *.sif images.

• Old Singularity versions may sporadically produce the error FATAL: could not open image jasen/container/*.sif: image format not recognized!

License

The Jasen documentation is distributed under GNU General Public License v3.