Modules/genes_collection.md

@@ -4,6 +4,7 @@ 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
@@ -23,6 +24,8 @@ The abundance information of the detected and clustered genes is then calculated
 
 The functional annotation of genes detected with prodigal is then carried out with [eggNOGG-mapper](https://github.com/eggnogdb/eggnog-mapper). The tool compares the input sequences with the eggnog database and assigns an orthologous group to each of these sequences, enabling them to be functionally annotated.
 
+A tool for the detection of MGEs (Mobile Genetic Elements) have also been added  with [genomad](https://github.com/apcamargo/genomad) to identify viruses and plasmids in sequencing data. The tool can be used in the [genomes collection](genomes_collection) but also in the genes collection part in a complementary way. 
+
 ### Genes taxonomic annotation ###
 
 After the clustered genes have been translated into proteins using [seqkit](https://github.com/shenwei356/seqkit), taxonomic annotation is performed using mmseqs2.