gemsweep — interactive pipeline diagram

Select a configuration to see which stages run. Dashed lines are bypass routes.

gemsweep pipeline diagram Shows which pipeline stages run based on selected reference mode, clustering method, and ref_prep_only. Input reads Provided index and groups ref_mode = index Reference list ref_mode = full / refine Sylph query GTDB ref_mode = autoselect Group by taxon Cluster references PopPUNK / core and accessory distances Derep to representatives Build Themisto index Run stops here Pseudoalign reads (Themisto) mSWEEP abundances mGEMS binning Binned reads output
Active this run Not used this run