full pipeline

The full workflow includes all the workflows outlined above with the addition of pangenome analysis using panaroo.

flowchart LR
fastq --> assembly --> annotation --> sequence_assessment
assembly --> speciation
fastq --> sequence_assessment --> report
fastq --> speciation --> report
speciation --> typing --> report
assembly --> typing
speciation --> AMR --> report
assembly --> AMR
assembly --> pangenome --> report
assembly -- "only possible with reference free" --> variant_detection
fastq --> variant_detection --> distances --> cluster --> report
variant_detection --> alignment --> tree_generation --> report

Like the comparative pipeline, you can select the comparative tool, tree builder, cluster methods, and thresholds. In addition, this pipeline will undertake the assembly, amr and typing described above and additional pangenome analysis.

For example

bohra run full -i input_file.tsv -j my_full_pipeline -ref <path_to_reference.fa(gbk)> --tree_builder iqtree --cluster_threshold 6,26