Just Another System for Epityping NGS data
Jasen produces results for antibiotic resistance and virulence prediction and epidemiological typing for surveillance purposes. The pipeline is developed in collaboration with several Swedish hospitals. The development was funded by Genomic Medicine Sweden.
The pipeline currently support a small set of microbiota and the support are in different stages of development. See the documentation of information on the supported analysis for each species and what the development status means.
| Species | Development status |
|---|---|
| Staphylococcus arueus | Stable |
| Escherichia coli | Stable |
| Mycobacterium tuberculosis | Stable |
| Klebsiella pneumoniae | Development |
| Streptococcus pyogenes | Stable |
| Streptococcus | Stable |
See the documentation for installation instructions.
- You can use Bonsai to visualise jasen outputs.
The documentation docs/source is available for the latest stable release.
Contributions to the pipeline is more than welcome. Please use the CONTRIBUTING file for details.
Jasen is released under the GPLv3 license.