Do I have to run the tools in the order of the tutorial?

The tools are presented in the order that a typical analysis would use. If you want to run some tools in parallel (to save time) you can do so. This workflow illustrates the analysis done in the tutorial and shows that there are multiple “paths” leading to outputs that have some steps that could be run at the same time: MultiQC, Kraken2, JBrowse and TB Variant Report.

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{% snippet  topics/variant-analysis/tutorials/tb-variant-analysis/faqs/tool_order.md %}

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