comparative pipeline

This workflow will run on fastq and/or fasta (depending user supplied input) and is the first step in all other workflows implmented by bohra. It can also be used alone as a simply quality control workflow.

flowchart LR
sequence --> sequence_assessment --> report
sequence --> speciation --> report
sequence --> sketch --> distances --> report
distances --> tree_generation --> report

Please take note - it will not run any assembly based tools, like MLST or AMR. If these are required use the full pipeline. There are three tools available in bohra that can be used for this purpose

bohra run preview -i input_file.tsv -j my_preview_pipeline --cpus X