Modules/assembly.md

 ---
 title: Assembly
 ---
+
 # Metagenomics assemblies #
 
 Metagenomics assemblies are almost inevitable in metagenomic analysis to reduce the fragmentation of informations and highlight sample characteristics. Reads are assembled into contigs using [megahit](https://github.com/voutcn/megahit) a fast assembler optimized for metagenomes and based on k-mers succinct de Bruijn graphs. Megahit is faster and perform comparably as SPAde and metaSPAdes. SPAde assemblies might be better in term of long contigs and ultra long contigs, it's also show a greater rate of missassemblies which required assembly curation [(1)](https://link.springer.com/article/10.1186/s12864-017-3918-9). 
@@ -16,19 +17,13 @@ For now, misasassemblies are only detected, therefore, if it's required, assembl
 
 Single-assembly is a per-sample approach where reads from one sample are assembled into one assembly. This approach is used by the genes_collection module and might be used by the genomes_collection module.
 
-```magneto run single-assembly **snakemake.args ```
+```magneto run single-assembly --config target=single_assembly **snakemake.args ```
 
 ## Co-assembly ##
 
 Co-assembly require the [simka module](Modules/simka). In this case, reads from each samples of a cluster are assembled together. This approach might be used by the genomes_collection module.
 
-```magneto run co-assembly **snakemake.args ```
-
-## Assembly ##
-
-Finally, both single-assembly and co-assembly might be ran using the following command line : 
-
-```magneto run assembly **snakemake.args ```
+```magneto run assembly --config target=co_assembly **snakemake.args ```
 
 -----
 [Previous - Simka (Module)](Modules/simka)