tb pipeline

bohra now has a M. tuberulosis specific workflow, which does not run MLST or other assembly based tools. And undertakes M. tuberculosis relevant gDST. It uses the H37rV reference genome, masking repetitive sites and tbtAMR for generation of an inferred antibiogram.

flowchart LR
fastq --> sequence_assessment --> report
fastq --> speciation --> report
speciation --> lineage --> report
fastq --> AMR --> report
fastq --> variant_detection --> distances --> cluster --> report
variant_detection --> alignment --> tree_generation --> report

The tb pipeline will run tools specific for M. tuberculosis, using tbtAMR (WHO v2 catalogue) for inferrence of resistance and the H37rV reference genome and mask

bohra tb -i input_file.tsv -j my_tb_pipeline