Modules/genes_collection.md

@@ -5,9 +5,10 @@ title: Genes collection
 
 
 
+
 Magneto makes it possible to obtain a genes collection directly from the assembly. This eliminates the need for binning and provides preliminary taxonomic and functional information (although this is less accurate than [genomes collection](Modules/genomes_collection)).
 ```
-magneto run genes_collection --config target=single_assembly **snakemake.args
+magneto run genes --config target=single_assembly **snakemake.args
 ```
 
 This step is only performed with single-assembly data. However, even if you choose to perform co-assembly, single-assembly can be performed on your data to obtain the gene collection. You may also not wish to create this genes collection, whether using single or co-assembly, this choice can be made in the config file by setting genes_collection to False.