Modules/genomes_collection.md

 ---
 title: Genomes collection
 ---
+
 At this stage of the workflow, we have a number of bins obtained from the assembly of sample reads. The next step is to check the quality of this bins, then obtain their abundance and annotate them functionally and taxonomically.
 
+```
+magneto run genomes --config target=single_assembly **snakemake.args
+```
+
 ### Genomes quality and dereplication ###
 
 Refinement is the first quality control carried out on bins. This stage is carried out using the [CheckM2](https://github.com/chklovski/CheckM2) tool, which estimates completeness and contamination based on the presence of single-copy marker genes(122 archaeal and 120 bacterial ), shared universally between prokaryotes, in the bins.