Pipelines overview
bohra has 6 pipelines which will use different combinations of modules to generate specific results.
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| Module | basic | preview | assemble | amr_typing | comparative | full | tb |
|---|---|---|---|---|---|---|---|
| Sequence assessment | Yes | Yes | Yes | Optional | Yes | Yes | Yes |
| Speciation | Optional | Optional | Optional | Optional | Optional | Optional | Optional |
| Assemble | No | No | Yes | Yes (if required) | No | Yes | No |
| MLST | No | No | No | Yes | No | Yes | No |
| Serotype | No | No | No | Yes (if speciation done) | No | Yes | No |
| AMR | No | No | No | Yes | No | Yes | Yes |
| Plasmid detection | No | No | No | Yes | No | Yes | No |
| Tree | No | Yes (default quicktree) | No | No | Yes (default iqtree) | Yes (default iqtree) | Yes (default iqtree) |
| Distance/comparative analysis | No | Yes (mash) | No | No | Yes (default snippy) | Yes (default snippy) | Yes (default snippy) |
| Pangenome | No | No | No | No | No | Yes | No |